Reading parmfile "parmfile.testml"....
WARNING: Inappropiate entry in parmfile: inheritance-scalars ignored
  =============================================
  MIGRATION RATE AND POPULATION SIZE ESTIMATION
  using Markov Chain Monte Carlo simulation
  =============================================
  Compiled for a PARALLEL COMPUTER ARCHITECTURE
  One master and 2 compute nodes are available.
  PDF output enabled [Letter-size]
  Version 3.1.4   [1685]
  Program started at   Wed May 12 12:30:04 2010




Reading (0) population__number___0 ...
Reading (1) population__number___1 ...


WARNING: Inappropiate entry in parmfile: inheritance-scalars ignored
1> population relabel [0]=1 (input: |1|)
WARNING: Inappropiate entry in parmfile: inheritance-scalars ignored
2> population relabel [0]=1 (input: |1|)
Options in use:
---------------

Analysis strategy is                          Maximum likelihood



Datatype: Microsatellite data [Brownian motion]
Missing data is not included

Pseudo-random number generator: Mersenne-Twister                                
Random number seed (from parmfile)           1407071073

Start parameters:
   First genealogy was started using a UPGMA-tree
   Theta values were generated  from an FST-calculation
   M values were generated from guessed values
   M-matrix: -----  1.00 
                1.00 ----- 
               

Migration model:
   Migration matrix model with variable Theta  

Mutation rate is constant for all loci

Markov chain settings:
   Short chains (short-chains):                           10
      Trees sampled (short-inc*samples):                1000
      Trees recorded (short-sample):                     500
   Long chains (long-chains):                              3
      Trees sampled (long-inc*samples):                 2000
      Trees recorded (long-sample):                     1000
   Averaging over replicates:                              2
   Static heating scheme
      4 chains with  temperatures
       1.00, 1.50, 3.00,1000000.00
      Swapping interval is 1
   Number of discard trees per chain:                   1000

Print options:
   Data file:                                    infile.msat
   Output file (ASCII text):                      outfile-ml
   Output file (PDF):                         outfile-ml.pdf
   Print data:                                            No
   Print genealogies:                                     No
   Plot data: No                                            
   Profile likelihood: Yes, tables and summary             
             Percentile method
             with df=1 and for Theta and M=m/mu




Summary of data:
Title:   Example: Microsatellite data set
Data file:             infile.msat
Datatype:               Microsatellite data
Number of loci:                          10

Population                   Locus   Gene copies    
                                     ---------------
                                     data  (missing)
----------------------------------------------------
  1 population__number___0       1     50 (0)
  1                              2     50 (0)
  1                              3     50 (0)
  1                              4     50 (0)
  1                              5     50 (0)
  1                              6     50 (0)
  1                              7     50 (0)
  1                              8     50 (0)
  1                              9     50 (0)
  1                             10     50 (0)
  2 population__number___1       1     42 (0)
  2                              2     42 (0)
  2                              3     42 (0)
  2                              4     42 (0)
  2                              5     42 (0)
  2                              6     42 (0)
  2                              7     42 (0)
  2                              8     42 (0)
  2                              9     42 (0)
  2                             10     42 (0)
    Total of all populations     1     92 (0)
                                 2     92 (0)
                                 3     92 (0)
                                 4     92 (0)
                                 5     92 (0)
                                 6     92 (0)
                                 7     92 (0)
                                 8     92 (0)
                                 9     92 (0)
                                10     92 (0)



[  1] Locus 1  : Replicate 1
[  1] 12:30:04   Burn-in (first 1000 trees are not used)


[  2] Locus 2  : Replicate 1
[  2] 12:30:04   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    indeterminate
12:30:04   [NODE:1] Locus 1: Short chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     13.20382  
           Start-tree-ln(L)=ln P(D|G):                 -47.19641
           Pop. Theta    M
             1  1.19692 ------    1.9 
             2  1.68463    2.1 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.16   |        0 ||
               1.5000  |   0.14   |        0  ||
               1.0000  |   0.13   |        0   |
[  1] 12:30:04   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    indeterminate
12:30:04   [NODE:2] Locus 2: Short chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.35752   
           Start-tree-ln(L)=ln P(D|G):                 -21.40418
           Pop. Theta    M
             1  1.28148 ------    0.9 
             2  0.94312    1.4 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.34   |        0 ||
               1.5000  |   0.32   |        0  ||
               1.0000  |   0.32   |        0   |
[  2] 12:30:04   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:30 May 12 2010
12:30:04   [NODE:1] Locus 1: Short chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     4.47017   
           Start-tree-ln(L)=ln P(D|G):                 -44.22010
           Pop. Theta    M
             1  1.55753 ------    1.6 
             2  2.36100    2.4 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000001
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.19   |        0 ||
               1.5000  |   0.14   |        0  ||
               1.0000  |   0.16   |        0   |
[  1] 12:30:04   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:05   [NODE:2] Locus 2: Short chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     5.05851   
           Start-tree-ln(L)=ln P(D|G):                 -25.32220
           Pop. Theta    M
             1  1.90493 ------    0.8 
             2  1.09299    2.4 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.35   |        0 ||
               1.5000  |   0.34   |        0  ||
               1.0000  |   0.36   |        0   |
[  2] 12:30:05   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:05   [NODE:1] Locus 1: Short chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.62379   
           Start-tree-ln(L)=ln P(D|G):                 -51.66207
           Pop. Theta    M
             1  2.05096 ------    2.0 
             2  2.93767    1.8 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.19   |        0 ||
               1.5000  |   0.15   |        0  ||
               1.0000  |   0.16   |        0   |
[  1] 12:30:05   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:05   [NODE:2] Locus 2: Short chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.03772   
           Start-tree-ln(L)=ln P(D|G):                 -32.66200
           Pop. Theta    M
             1  2.08486 ------    0.7 
             2  1.37489    2.2 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.37   |        0 ||
               1.5000  |   0.34   |        0  ||
               1.0000  |   0.31   |        0   |
[  2] 12:30:05   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:05   [NODE:1] Locus 1: Short chain   4:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.67697   
           Start-tree-ln(L)=ln P(D|G):                 -55.29319
           Pop. Theta    M
             1  2.53518 ------    1.9 
             2  3.85743    2.0 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.15   |        0 ||
               1.5000  |   0.15   |        0  ||
               1.0000  |   0.17   |        0   |
[  1] 12:30:05   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:30 May 12 2010
12:30:05   [NODE:2] Locus 2: Short chain   4:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.85067   
           Start-tree-ln(L)=ln P(D|G):                 -32.78792
           Pop. Theta    M
             1  2.26866 ------    0.4 
             2  1.17063    3.5 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.39   |        0 ||
               1.5000  |   0.34   |        0  ||
               1.0000  |   0.34   |        0   |
[  2] 12:30:05   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:30 May 12 2010
12:30:05   [NODE:1] Locus 1: Short chain   5:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.88104   
           Start-tree-ln(L)=ln P(D|G):                 -45.62216
           Pop. Theta    M
             1  2.89699 ------    1.8 
             2  4.36394    2.6 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.18   |        0 ||
               1.5000  |   0.17   |        0  ||
               1.0000  |   0.18   |        0   |
[  1] 12:30:05   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:30 May 12 2010
12:30:05   [NODE:2] Locus 2: Short chain   5:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.94951   
           Start-tree-ln(L)=ln P(D|G):                 -37.21880
           Pop. Theta    M
             1  2.58153 ------    0.8 
             2  1.55265    2.8 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.39   |        0 ||
               1.5000  |   0.37   |        0  ||
               1.0000  |   0.32   |        0   |
[  2] 12:30:05   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:06   [NODE:1] Locus 1: Short chain   6:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.56067   
           Start-tree-ln(L)=ln P(D|G):                 -62.58217
           Pop. Theta    M
             1  3.57797 ------    1.9 
             2  3.88975    2.0 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.16   |        0 ||
               1.5000  |   0.16   |        0  ||
               1.0000  |   0.18   |        0   |
[  1] 12:30:06   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:06   [NODE:2] Locus 2: Short chain   6:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.55838   
           Start-tree-ln(L)=ln P(D|G):                 -39.55408
           Pop. Theta    M
             1  2.86852 ------    0.7 
             2  1.59549    3.5 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.39   |        0 ||
               1.5000  |   0.35   |        0  ||
               1.0000  |   0.34   |        0   |
[  2] 12:30:06   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:06   [NODE:1] Locus 1: Short chain   7:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.24341   
           Start-tree-ln(L)=ln P(D|G):                 -62.49202
           Pop. Theta    M
             1  3.66633 ------    1.9 
             2  5.03440    2.0 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.18   |        0 ||
               1.5000  |   0.15   |        0  ||
               1.0000  |   0.18   |        0   |
[  1] 12:30:06   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:30 May 12 2010
12:30:06   [NODE:2] Locus 2: Short chain   7:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.05427   
           Start-tree-ln(L)=ln P(D|G):                 -33.91265
           Pop. Theta    M
             1  2.63311 ------    0.6 
             2  2.33328    2.8 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.39   |        0 ||
               1.5000  |   0.35   |        0  ||
               1.0000  |   0.34   |        0   |
[  2] 12:30:06   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:30 May 12 2010
12:30:06   [NODE:1] Locus 1: Short chain   8:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.68181   
           Start-tree-ln(L)=ln P(D|G):                 -58.86431
           Pop. Theta    M
             1  3.22083 ------    2.1 
             2  5.78825    1.9 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000001
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.17   |        0 ||
               1.5000  |   0.15   |        0  ||
               1.0000  |   0.17   |        0   |
[  1] 12:30:06   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:30 May 12 2010
12:30:06   [NODE:2] Locus 2: Short chain   8:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.15950   
           Start-tree-ln(L)=ln P(D|G):                 -31.50461
           Pop. Theta    M
             1  3.61698 ------    0.7 
             2  2.23903    1.8 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.40   |        0 ||
               1.5000  |   0.33   |        0  ||
               1.0000  |   0.33   |        0   |
[  2] 12:30:06   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:07   [NODE:1] Locus 1: Short chain   9:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.36752   
           Start-tree-ln(L)=ln P(D|G):                 -85.31240
           Pop. Theta    M
             1  3.79044 ------    2.1 
             2  5.36118    2.6 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.19   |        0 ||
               1.5000  |   0.15   |        0  ||
               1.0000  |   0.19   |        0   |
[  1] 12:30:07   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:07   [NODE:2] Locus 2: Short chain   9:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.41449   
           Start-tree-ln(L)=ln P(D|G):                 -39.23025
           Pop. Theta    M
             1  3.96049 ------    1.4 
             2  1.80676    2.0 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.36   |        0 ||
               1.5000  |   0.31   |        0  ||
               1.0000  |   0.33   |        0   |
[  2] 12:30:07   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:07   [NODE:1] Locus 1: Short chain  10:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.35156   
           Start-tree-ln(L)=ln P(D|G):                 -74.06433
           Pop. Theta    M
             1  5.10041 ------    2.0 
             2  6.28757    2.1 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.17   |        0 ||
               1.5000  |   0.15   |        0  ||
               1.0000  |   0.20   |        0   |
[  1] 12:30:07   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:30 May 12 2010
12:30:07   [NODE:2] Locus 2: Short chain  10:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     5.00988   
           Start-tree-ln(L)=ln P(D|G):                 -43.96355
           Pop. Theta    M
             1  3.73365 ------    1.5 
             2  1.84256    4.3 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.35   |        0 ||
               1.5000  |   0.30   |        0  ||
               1.0000  |   0.30   |        0   |
[  2] 12:30:07   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:08   [NODE:1] Locus 1: Long chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.89204   
           Start-tree-ln(L)=ln P(D|G):                 -73.65096
           Pop. Theta    M
             1  4.69093 ------    2.1 
             2  6.43621    2.9 ------ 
 
           Maximization cycles needed: 15
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.18   |        0 ||
               1.5000  |   0.16   |        0  ||
               1.0000  |   0.21   |        0   |
[  1] 12:30:08   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:08   [NODE:2] Locus 2: Long chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.96498   
           Start-tree-ln(L)=ln P(D|G):                 -39.73656
           Pop. Theta    M
             1  3.16958 ------    1.6 
             2  2.31438    3.8 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.38   |        0 ||
               1.5000  |   0.31   |        0  ||
               1.0000  |   0.34   |        0   |
[  2] 12:30:08   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:08   [NODE:1] Locus 1: Long chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.62067   
           Start-tree-ln(L)=ln P(D|G):                 -65.68529
           Pop. Theta    M
             1  5.41421 ------    2.2 
             2  8.58799    2.8 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.19   |        0 ||
               1.5000  |   0.16   |        0  ||
               1.0000  |   0.19   |        0   |
[  1] 12:30:08   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:08   [NODE:2] Locus 2: Long chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.78837   
           Start-tree-ln(L)=ln P(D|G):                 -32.42747
           Pop. Theta    M
             1  3.46331 ------    1.5 
             2  1.98454    3.0 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.38   |        0 ||
               1.5000  |   0.31   |        0  ||
               1.0000  |   0.35   |        0   |
[  2] 12:30:08   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:09   [NODE:1] Locus 1: Long chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.05371   
           Start-tree-ln(L)=ln P(D|G):                 -53.56676
           Pop. Theta    M
             1  4.85193 ------    1.8 
             2  9.59602    2.6 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.19   |        0 ||
               1.5000  |   0.13   |        0  ||
               1.0000  |   0.18   |        0   |


[  1] Locus 1  : Replicate 2
[  1] 12:30:09   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:09   [NODE:2] Locus 2: Long chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.70870   
           Start-tree-ln(L)=ln P(D|G):                 -36.87799
           Pop. Theta    M
             1  2.64046 ------    1.1 
             2  1.71004    3.7 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.36   |        0 ||
               1.5000  |   0.33   |        0  ||
               1.0000  |   0.33   |        0   |


[  2] Locus 2  : Replicate 2
[  2] 12:30:09   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:09   [NODE:1] Locus 1: Short chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     10.23416  
           Start-tree-ln(L)=ln P(D|G):                 -51.17981
           Pop. Theta    M
             1  1.42803 ------    2.6 
             2  1.27974    1.6 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.19   |        0 ||
               1.5000  |   0.13   |        0  ||
               1.0000  |   0.15   |        0   |
[  1] 12:30:09   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:09   [NODE:2] Locus 2: Short chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.71878   
           Start-tree-ln(L)=ln P(D|G):                 -21.48103
           Pop. Theta    M
             1  1.16373 ------    1.8 
             2  1.32320    1.2 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.37   |        0 ||
               1.5000  |   0.32   |        0  ||
               1.0000  |   0.33   |        0   |
[  2] 12:30:09   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:09   [NODE:1] Locus 1: Short chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.09784   
           Start-tree-ln(L)=ln P(D|G):                 -49.95347
           Pop. Theta    M
             1  1.46517 ------    1.7 
             2  1.47395    1.6 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.19   |        0 ||
               1.5000  |   0.12   |        0  ||
               1.0000  |   0.14   |        0   |
[  1] 12:30:09   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:10   [NODE:2] Locus 2: Short chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.56732   
           Start-tree-ln(L)=ln P(D|G):                 -22.91981
           Pop. Theta    M
             1  1.26534 ------    1.0 
             2  1.45618    1.9 ------ 
 
           Maximization cycles needed: 13
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.35   |        0 ||
               1.5000  |   0.34   |        0  ||
               1.0000  |   0.32   |        0   |
[  2] 12:30:10   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:10   [NODE:1] Locus 1: Short chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     5.81594   
           Start-tree-ln(L)=ln P(D|G):                 -55.61639
           Pop. Theta    M
             1  1.42718 ------    2.6 
             2  1.90522    2.7 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.18   |        0 ||
               1.5000  |   0.12   |        0  ||
               1.0000  |   0.15   |        0   |
[  1] 12:30:10   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:10   [NODE:2] Locus 2: Short chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.64490   
           Start-tree-ln(L)=ln P(D|G):                 -31.98657
           Pop. Theta    M
             1  1.39561 ------    1.8 
             2  1.96006    3.1 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.36   |        0 ||
               1.5000  |   0.34   |        0  ||
               1.0000  |   0.34   |        0   |
[  2] 12:30:10   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:10   [NODE:1] Locus 1: Short chain   4:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     16.96096  
           Start-tree-ln(L)=ln P(D|G):                 -51.61450
           Pop. Theta    M
             1  1.50602 ------    1.4 
             2  2.46021    0.8 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000001
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.18   |        0 ||
               1.5000  |   0.14   |        0  ||
               1.0000  |   0.16   |        0   |
[  1] 12:30:10   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:10   [NODE:1] Locus 1: Short chain   5:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     5.09775   
           Start-tree-ln(L)=ln P(D|G):                 -66.12618
           Pop. Theta    M
             1  1.78645 ------    1.9 
             2  2.98813    1.4 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.16   |        0 ||
               1.5000  |   0.12   |        0  ||
               1.0000  |   0.17   |        0   |
[  1] 12:30:10   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:10   [NODE:2] Locus 2: Short chain   4:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.35114   
           Start-tree-ln(L)=ln P(D|G):                 -29.29798
           Pop. Theta    M
             1  1.65025 ------    1.5 
             2  2.98140    3.4 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.37   |        0 ||
               1.5000  |   0.32   |        0  ||
               1.0000  |   0.35   |        0   |
[  2] 12:30:10   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:10   [NODE:1] Locus 1: Short chain   6:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.60453   
           Start-tree-ln(L)=ln P(D|G):                 -55.39671
           Pop. Theta    M
             1  1.90206 ------    2.2 
             2  3.24156    1.5 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.16   |        0 ||
               1.5000  |   0.14   |        0  ||
               1.0000  |   0.16   |        0   |
[  1] 12:30:10   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:11   [NODE:2] Locus 2: Short chain   5:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.19883   
           Start-tree-ln(L)=ln P(D|G):                 -38.76856
           Pop. Theta    M
             1  1.80508 ------    2.1 
             2  2.50227    2.8 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.37   |        0 ||
               1.5000  |   0.34   |        0  ||
               1.0000  |   0.33   |        0   |
[  2] 12:30:11   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:11   [NODE:1] Locus 1: Short chain   7:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.68991   
           Start-tree-ln(L)=ln P(D|G):                 -64.01955
           Pop. Theta    M
             1  2.06787 ------    2.3 
             2  3.85831    1.5 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.17   |        0 ||
               1.5000  |   0.15   |        0  ||
               1.0000  |   0.14   |        0   |
[  1] 12:30:11   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:11   [NODE:2] Locus 2: Short chain   6:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.89055   
           Start-tree-ln(L)=ln P(D|G):                 -34.34825
           Pop. Theta    M
             1  2.01397 ------    2.2 
             2  1.43638    2.9 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.41   |        0 ||
               1.5000  |   0.34   |        0  ||
               1.0000  |   0.32   |        0   |
[  2] 12:30:11   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:11   [NODE:1] Locus 1: Short chain   8:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.02205   
           Start-tree-ln(L)=ln P(D|G):                 -67.95274
           Pop. Theta    M
             1  2.17816 ------    2.1 
             2  4.52512    1.3 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.13   |        0 ||
               1.5000  |   0.15   |        0  ||
               1.0000  |   0.16   |        0   |
[  1] 12:30:11   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:11   [NODE:2] Locus 2: Short chain   7:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.44701   
           Start-tree-ln(L)=ln P(D|G):                 -37.01825
           Pop. Theta    M
             1  2.49603 ------    2.4 
             2  1.74723    2.1 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.39   |        0 ||
               1.5000  |   0.35   |        0  ||
               1.0000  |   0.31   |        0   |
[  2] 12:30:11   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:11   [NODE:1] Locus 1: Short chain   9:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.22433   
           Start-tree-ln(L)=ln P(D|G):                 -62.85111
           Pop. Theta    M
             1  2.27613 ------    3.0 
             2  5.07710    1.2 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000001
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.14   |        0 ||
               1.5000  |   0.15   |        0  ||
               1.0000  |   0.19   |        0   |
[  1] 12:30:11   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:12   [NODE:2] Locus 2: Short chain   8:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.34042   
           Start-tree-ln(L)=ln P(D|G):                 -42.74545
           Pop. Theta    M
             1  2.51084 ------    2.1 
             2  1.97467    2.2 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.37   |        0 ||
               1.5000  |   0.35   |        0  ||
               1.0000  |   0.33   |        0   |
[  2] 12:30:12   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:12   [NODE:1] Locus 1: Short chain  10:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.88064   
           Start-tree-ln(L)=ln P(D|G):                 -57.74543
           Pop. Theta    M
             1  2.13439 ------    2.5 
             2  5.80714    1.2 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.16   |        0 ||
               1.5000  |   0.12   |        0  ||
               1.0000  |   0.16   |        0   |
[  1] 12:30:12   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:12   [NODE:2] Locus 2: Short chain   9:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.32401   
           Start-tree-ln(L)=ln P(D|G):                 -41.02210
           Pop. Theta    M
             1  3.12514 ------    1.8 
             2  2.23621    1.9 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.38   |        0 ||
               1.5000  |   0.35   |        0  ||
               1.0000  |   0.32   |        0   |
[  2] 12:30:12   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:12   [NODE:2] Locus 2: Short chain  10:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.48361   
           Start-tree-ln(L)=ln P(D|G):                 -48.33365
           Pop. Theta    M
             1  4.64309 ------    2.2 
             2  1.83028    2.0 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.39   |        0 ||
               1.5000  |   0.33   |        0  ||
               1.0000  |   0.38   |        0   |
[  2] 12:30:12   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:12   [NODE:1] Locus 1: Long chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.82490   
           Start-tree-ln(L)=ln P(D|G):                 -64.73548
           Pop. Theta    M
             1  2.03777 ------    2.7 
             2  7.36498    1.5 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.15   |        0 ||
               1.5000  |   0.14   |        0  ||
               1.0000  |   0.15   |        0   |
[  1] 12:30:12   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:13   [NODE:1] Locus 1: Long chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.71065   
           Start-tree-ln(L)=ln P(D|G):                 -56.84617
           Pop. Theta    M
             1  2.09842 ------    3.1 
             2  5.18472    1.7 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.16   |        0 ||
               1.5000  |   0.14   |        0  ||
               1.0000  |   0.15   |        0   |
[  1] 12:30:13   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:13   [NODE:2] Locus 2: Long chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.50393   
           Start-tree-ln(L)=ln P(D|G):                 -39.97938
           Pop. Theta    M
             1  5.02573 ------    1.7 
             2  1.98897    1.9 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.38   |        0 ||
               1.5000  |   0.36   |        0  ||
               1.0000  |   0.38   |        0   |
[  2] 12:30:13   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:13   [NODE:1] Locus 1: Long chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.79503   
           Start-tree-ln(L)=ln P(D|G):                 -58.47615
           Pop. Theta    M
             1  2.77115 ------    3.3 
             2  7.07081    1.6 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.17   |        0 ||
               1.5000  |   0.15   |        0  ||
               1.0000  |   0.16   |        0   |
           Prognosed end of sampling is    12:31 May 12 2010
12:30:13   Multiple chain estimates:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     5.59007   
           Pop. Theta    M
             1  2.77115 ------    3.3 
             2  7.07081    1.6 ------ 
 
           Maximization cycles needed: 0
           Norm of first derivatives:  0.000000


[  1] Locus 3  : Replicate 1
[  1] 12:30:13   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:13   [NODE:2] Locus 2: Long chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.68062   
           Start-tree-ln(L)=ln P(D|G):                 -42.41194
           Pop. Theta    M
             1  3.60399 ------    2.3 
             2  1.98203    1.4 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.38   |        0 ||
               1.5000  |   0.34   |        0  ||
               1.0000  |   0.37   |        0   |
[  2] 12:30:13   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:14   [NODE:1] Locus 3: Short chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.66657   
           Start-tree-ln(L)=ln P(D|G):                 -21.68566
           Pop. Theta    M
             1  1.07648 ------    1.5 
             2  0.76324    1.0 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.35   |        0 ||
               1.5000  |   0.28   |        0  ||
               1.0000  |   0.27   |        0   |
[  1] 12:30:14   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:14   [NODE:1] Locus 3: Short chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.06185   
           Start-tree-ln(L)=ln P(D|G):                 -19.99075
           Pop. Theta    M
             1  0.87814 ------    2.0 
             2  0.92029    1.1 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.32   |        0 ||
               1.5000  |   0.29   |        0  ||
               1.0000  |   0.27   |        0   |
[  1] 12:30:14   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:14   [NODE:2] Locus 2: Long chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.73575   
           Start-tree-ln(L)=ln P(D|G):                 -40.63041
           Pop. Theta    M
             1  3.30446 ------    1.7 
             2  2.42257    2.3 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.40   |        0 ||
               1.5000  |   0.34   |        0  ||
               1.0000  |   0.34   |        0   |
           Prognosed end of sampling is    12:31 May 12 2010
12:30:14   Multiple chain estimates:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.23723   
           Pop. Theta    M
             1  3.43558 ------    2.0 
             2  2.19356    1.8 ------ 
 
           Maximization cycles needed: 14
           Norm of first derivatives:  0.000000


[  2] Locus 4  : Replicate 1
[  2] 12:30:14   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:14   [NODE:1] Locus 3: Short chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.84627   
           Start-tree-ln(L)=ln P(D|G):                 -16.02909
           Pop. Theta    M
             1  1.13333 ------    2.3 
             2  1.02166    0.9 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.33   |        0 ||
               1.5000  |   0.30   |        0  ||
               1.0000  |   0.29   |        0   |
[  1] 12:30:14   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:14   [NODE:2] Locus 4: Short chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     13.41127  
           Start-tree-ln(L)=ln P(D|G):                 -56.59903
           Pop. Theta    M
             1  1.40537 ------    2.1 
             2  1.29774    2.2 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.14   |        0 ||
               1.5000  |   0.10   |        0  ||
               1.0000  |   0.12   |        0   |
[  2] 12:30:14   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:15   [NODE:1] Locus 3: Short chain   4:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.43687   
           Start-tree-ln(L)=ln P(D|G):                 -16.90597
           Pop. Theta    M
             1  0.82872 ------    2.7 
             2  1.08169    1.1 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.34   |        0 ||
               1.5000  |   0.33   |        0  ||
               1.0000  |   0.29   |        0   |
[  1] 12:30:15   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:15   [NODE:2] Locus 4: Short chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.80057   
           Start-tree-ln(L)=ln P(D|G):                 -55.21426
           Pop. Theta    M
             1  1.42941 ------    1.7 
             2  1.66279    1.9 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.13   |        0 ||
               1.5000  |   0.10   |        0  ||
               1.0000  |   0.12   |        0   |
[  2] 12:30:15   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:15   [NODE:1] Locus 3: Short chain   5:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.06640   
           Start-tree-ln(L)=ln P(D|G):                 -19.67695
           Pop. Theta    M
             1  1.08461 ------    2.9 
             2  0.93986    1.0 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000001
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.34   |        0 ||
               1.5000  |   0.30   |        0  ||
               1.0000  |   0.29   |        0   |
[  1] 12:30:15   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:15   [NODE:2] Locus 4: Short chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     5.31832   
           Start-tree-ln(L)=ln P(D|G):                 -53.95183
           Pop. Theta    M
             1  2.04145 ------    1.5 
             2  2.23540    2.0 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.12   |        0 ||
               1.5000  |   0.11   |        0  ||
               1.0000  |   0.12   |        0   |
[  2] 12:30:15   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:15   [NODE:1] Locus 3: Short chain   6:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     5.37484   
           Start-tree-ln(L)=ln P(D|G):                 -19.08149
           Pop. Theta    M
             1  0.99518 ------    5.2 
             2  1.25484    1.6 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000001
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.36   |        0 ||
               1.5000  |   0.29   |        0  ||
               1.0000  |   0.28   |        0   |
[  1] 12:30:15   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:15   [NODE:2] Locus 4: Short chain   4:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.96295   
           Start-tree-ln(L)=ln P(D|G):                 -44.73474
           Pop. Theta    M
             1  2.68582 ------    2.2 
             2  2.29455    1.7 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.12   |        0 ||
               1.5000  |   0.12   |        0  ||
               1.0000  |   0.13   |        0   |
[  2] 12:30:15   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:16   [NODE:1] Locus 3: Short chain   7:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.66490   
           Start-tree-ln(L)=ln P(D|G):                 -20.06299
           Pop. Theta    M
             1  0.80705 ------    5.5 
             2  1.21516    2.5 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.36   |        0 ||
               1.5000  |   0.29   |        0  ||
               1.0000  |   0.29   |        0   |
[  1] 12:30:16   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:16   [NODE:2] Locus 4: Short chain   5:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.88077   
           Start-tree-ln(L)=ln P(D|G):                 -57.58166
           Pop. Theta    M
             1  3.38347 ------    2.4 
             2  3.06006    2.1 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.12   |        0 ||
               1.5000  |   0.11   |        0  ||
               1.0000  |   0.12   |        0   |
[  2] 12:30:16   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:16   [NODE:2] Locus 4: Short chain   6:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     4.59230   
           Start-tree-ln(L)=ln P(D|G):                 -50.96189
           Pop. Theta    M
             1  4.36946 ------    3.0 
             2  3.93711    1.8 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.12   |        0 ||
               1.5000  |   0.09   |        0  ||
               1.0000  |   0.13   |        0   |
[  2] 12:30:16   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:16   [NODE:1] Locus 3: Short chain   8:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.31078   
           Start-tree-ln(L)=ln P(D|G):                 -28.69346
           Pop. Theta    M
             1  1.05772 ------    5.0 
             2  0.91804    2.9 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.35   |        0 ||
               1.5000  |   0.30   |        0  ||
               1.0000  |   0.29   |        0   |
[  1] 12:30:16   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:16   [NODE:2] Locus 4: Short chain   7:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.15964   
           Start-tree-ln(L)=ln P(D|G):                 -60.43080
           Pop. Theta    M
             1  6.04718 ------    3.2 
             2  4.32968    1.9 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.14   |        0 ||
               1.5000  |   0.10   |        0  ||
               1.0000  |   0.13   |        0   |
[  2] 12:30:16   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:16   [NODE:1] Locus 3: Short chain   9:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.41349   
           Start-tree-ln(L)=ln P(D|G):                 -12.21566
           Pop. Theta    M
             1  0.92052 ------    7.4 
             2  0.96272    4.3 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000001
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.37   |        0 ||
               1.5000  |   0.31   |        0  ||
               1.0000  |   0.31   |        0   |
[  1] 12:30:16   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:17   [NODE:2] Locus 4: Short chain   8:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.22927   
           Start-tree-ln(L)=ln P(D|G):                 -61.58347
           Pop. Theta    M
             1  7.79187 ------    3.0 
             2  4.15916    1.7 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.12   |        0 ||
               1.5000  |   0.11   |        0  ||
               1.0000  |   0.15   |        0   |
[  2] 12:30:17   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:17   [NODE:1] Locus 3: Short chain  10:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.54612   
           Start-tree-ln(L)=ln P(D|G):                 -19.50289
           Pop. Theta    M
             1  0.93105 ------    5.8 
             2  0.93517    5.7 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.33   |        0 ||
               1.5000  |   0.28   |        0  ||
               1.0000  |   0.27   |        0   |
[  1] 12:30:17   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:17   [NODE:2] Locus 4: Short chain   9:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.89173   
           Start-tree-ln(L)=ln P(D|G):                 -77.62629
           Pop. Theta    M
             1  9.76459 ------    2.9 
             2  5.54302    1.9 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.11   |        0 ||
               1.5000  |   0.13   |        0  ||
               1.0000  |   0.16   |        0   |
[  2] 12:30:17   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:17   [NODE:2] Locus 4: Short chain  10:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.50937   
           Start-tree-ln(L)=ln P(D|G):                 -76.38850
           Pop. Theta    M
             1  9.55958 ------    2.5 
             2  5.67656    2.0 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.14   |        0 ||
               1.5000  |   0.11   |        0  ||
               1.0000  |   0.14   |        0   |
[  2] 12:30:17   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:17   [NODE:1] Locus 3: Long chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.95053   
           Start-tree-ln(L)=ln P(D|G):                 -15.31896
           Pop. Theta    M
             1  0.99695 ------    6.1 
             2  1.41147    4.4 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.33   |        0 ||
               1.5000  |   0.34   |        0  ||
               1.0000  |   0.26   |        0   |
[  1] 12:30:17   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:18   [NODE:2] Locus 4: Long chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.29920   
           Start-tree-ln(L)=ln P(D|G):                 -69.62268
           Pop. Theta    M
             1  10.63264 ------    2.9 
             2  6.38433    1.8 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.13   |        0 ||
               1.5000  |   0.12   |        0  ||
               1.0000  |   0.17   |        0   |
[  2] 12:30:18   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:18   [NODE:1] Locus 3: Long chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.80817   
           Start-tree-ln(L)=ln P(D|G):                 -17.11970
           Pop. Theta    M
             1  1.20320 ------    5.8 
             2  1.55412    5.8 ------ 
 
           Maximization cycles needed: 13
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.33   |        0 ||
               1.5000  |   0.30   |        0  ||
               1.0000  |   0.30   |        0   |
[  1] 12:30:18   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:18   [NODE:2] Locus 4: Long chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.64984   
           Start-tree-ln(L)=ln P(D|G):                 -81.72242
           Pop. Theta    M
             1  12.49451 ------    2.3 
             2  7.05178    1.9 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.12   |        0 ||
               1.5000  |   0.11   |        0  ||
               1.0000  |   0.15   |        0   |
[  2] 12:30:18   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:19   [NODE:1] Locus 3: Long chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.05795   
           Start-tree-ln(L)=ln P(D|G):                 -21.20336
           Pop. Theta    M
             1  1.19139 ------    6.2 
             2  2.19207    5.0 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.32   |        0 ||
               1.5000  |   0.32   |        0  ||
               1.0000  |   0.29   |        0   |


[  1] Locus 3  : Replicate 2
[  1] 12:30:19   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:20   [NODE:2] Locus 4: Long chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.63591   
           Start-tree-ln(L)=ln P(D|G):                 -75.45286
           Pop. Theta    M
             1  9.01072 ------    2.3 
             2  7.17089    1.6 ------ 
 
           Maximization cycles needed: 13
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.13   |        0 ||
               1.5000  |   0.13   |        0  ||
               1.0000  |   0.16   |        0   |


[  2] Locus 4  : Replicate 2
[  2] 12:30:20   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:20   [NODE:1] Locus 3: Short chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     9.70755   
           Start-tree-ln(L)=ln P(D|G):                 -19.64533
           Pop. Theta    M
             1  1.18576 ------    2.1 
             2  1.12335    3.5 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.35   |        0 ||
               1.5000  |   0.29   |        0  ||
               1.0000  |   0.27   |        0   |
[  1] 12:30:20   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:20   [NODE:2] Locus 4: Short chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     16.61351  
           Start-tree-ln(L)=ln P(D|G):                 -54.87073
           Pop. Theta    M
             1  1.62589 ------    2.2 
             2  1.53856    1.6 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.12   |        0 ||
               1.5000  |   0.12   |        0  ||
               1.0000  |   0.10   |        0   |
[  2] 12:30:20   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:20   [NODE:1] Locus 3: Short chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     6.57129   
           Start-tree-ln(L)=ln P(D|G):                 -19.61909
           Pop. Theta    M
             1  1.80131 ------    2.9 
             2  1.47151    3.8 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.36   |        0 ||
               1.5000  |   0.33   |        0  ||
               1.0000  |   0.29   |        0   |
[  1] 12:30:20   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:20   [NODE:2] Locus 4: Short chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     5.36789   
           Start-tree-ln(L)=ln P(D|G):                 -54.67897
           Pop. Theta    M
             1  2.41877 ------    3.1 
             2  1.71305    1.1 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.12   |        0 ||
               1.5000  |   0.11   |        0  ||
               1.0000  |   0.11   |        0   |
[  2] 12:30:20   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:20   [NODE:1] Locus 3: Short chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.79513   
           Start-tree-ln(L)=ln P(D|G):                 -27.14518
           Pop. Theta    M
             1  2.06423 ------    2.6 
             2  1.20466    3.5 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.34   |        0 ||
               1.5000  |   0.31   |        0  ||
               1.0000  |   0.29   |        0   |
[  1] 12:30:20   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:21   [NODE:2] Locus 4: Short chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.06846   
           Start-tree-ln(L)=ln P(D|G):                 -63.94063
           Pop. Theta    M
             1  3.16212 ------    3.3 
             2  2.00540    1.2 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.12   |        0 ||
               1.5000  |   0.10   |        0  ||
               1.0000  |   0.13   |        0   |
[  2] 12:30:21   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:21   [NODE:1] Locus 3: Short chain   4:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.32076   
           Start-tree-ln(L)=ln P(D|G):                 -24.06636
           Pop. Theta    M
             1  2.25109 ------    2.5 
             2  0.90031    5.3 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000001
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.37   |        0 ||
               1.5000  |   0.29   |        0  ||
               1.0000  |   0.30   |        0   |
[  1] 12:30:21   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:21   [NODE:2] Locus 4: Short chain   4:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     6.64331   
           Start-tree-ln(L)=ln P(D|G):                 -68.51078
           Pop. Theta    M
             1  4.46948 ------    4.4 
             2  2.88343    1.1 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.11   |        0 ||
               1.5000  |   0.11   |        0  ||
               1.0000  |   0.13   |        0   |
[  2] 12:30:21   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:21   [NODE:1] Locus 3: Short chain   5:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.70057   
           Start-tree-ln(L)=ln P(D|G):                 -24.06729
           Pop. Theta    M
             1  1.90635 ------    2.6 
             2  0.94018    5.8 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.34   |        0 ||
               1.5000  |   0.30   |        0  ||
               1.0000  |   0.30   |        0   |
[  1] 12:30:21   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:21   [NODE:2] Locus 4: Short chain   5:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.25818   
           Start-tree-ln(L)=ln P(D|G):                 -59.95509
           Pop. Theta    M
             1  3.78282 ------    4.1 
             2  3.23625    1.3 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.15   |        0 ||
               1.5000  |   0.10   |        0  ||
               1.0000  |   0.12   |        0   |
[  2] 12:30:21   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:22   [NODE:1] Locus 3: Short chain   6:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.88571   
           Start-tree-ln(L)=ln P(D|G):                 -35.53178
           Pop. Theta    M
             1  2.25674 ------    2.3 
             2  1.01093    4.4 ------ 
 
           Maximization cycles needed: 14
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.35   |        0 ||
               1.5000  |   0.27   |        0  ||
               1.0000  |   0.29   |        0   |
[  1] 12:30:22   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:22   [NODE:2] Locus 4: Short chain   6:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.03992   
           Start-tree-ln(L)=ln P(D|G):                 -56.38271
           Pop. Theta    M
             1  4.10525 ------    4.1 
             2  4.42729    1.4 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.14   |        0 ||
               1.5000  |   0.10   |        0  ||
               1.0000  |   0.13   |        0   |
[  2] 12:30:22   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:22   [NODE:1] Locus 3: Short chain   7:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.97174   
           Start-tree-ln(L)=ln P(D|G):                 -25.19387
           Pop. Theta    M
             1  2.64734 ------    1.5 
             2  0.80043    4.5 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000001
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.34   |        0 ||
               1.5000  |   0.30   |        0  ||
               1.0000  |   0.31   |        0   |
[  1] 12:30:22   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:22   [NODE:2] Locus 4: Short chain   7:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.87443   
           Start-tree-ln(L)=ln P(D|G):                 -59.23711
           Pop. Theta    M
             1  5.06458 ------    3.5 
             2  3.75411    1.4 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.14   |        0 ||
               1.5000  |   0.13   |        0  ||
               1.0000  |   0.12   |        0   |
[  2] 12:30:22   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:22   [NODE:1] Locus 3: Short chain   8:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.96069   
           Start-tree-ln(L)=ln P(D|G):                 -28.45422
           Pop. Theta    M
             1  2.46879 ------    2.4 
             2  0.56685    3.3 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000001
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.32   |        0 ||
               1.5000  |   0.30   |        0  ||
               1.0000  |   0.29   |        0   |
[  1] 12:30:22   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:22   [NODE:2] Locus 4: Short chain   8:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     4.70229   
           Start-tree-ln(L)=ln P(D|G):                 -71.71696
           Pop. Theta    M
             1  7.68816 ------    3.6 
             2  5.09920    1.4 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.13   |        0 ||
               1.5000  |   0.11   |        0  ||
               1.0000  |   0.13   |        0   |
[  2] 12:30:22   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:22   [NODE:1] Locus 3: Short chain   9:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.44130   
           Start-tree-ln(L)=ln P(D|G):                 -25.01235
           Pop. Theta    M
             1  2.00905 ------    2.6 
             2  0.74721    4.1 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.33   |        0 ||
               1.5000  |   0.32   |        0  ||
               1.0000  |   0.29   |        0   |
[  1] 12:30:22   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:23   [NODE:2] Locus 4: Short chain   9:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.80607   
           Start-tree-ln(L)=ln P(D|G):                 -60.93490
           Pop. Theta    M
             1  6.48930 ------    3.8 
             2  5.53625    1.6 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.13   |        0 ||
               1.5000  |   0.12   |        0  ||
               1.0000  |   0.14   |        0   |
[  2] 12:30:23   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:23   [NODE:1] Locus 3: Short chain  10:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.22895   
           Start-tree-ln(L)=ln P(D|G):                 -23.13929
           Pop. Theta    M
             1  2.05542 ------    3.3 
             2  1.08449    5.1 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.33   |        0 ||
               1.5000  |   0.27   |        0  ||
               1.0000  |   0.31   |        0   |
[  1] 12:30:23   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:23   [NODE:2] Locus 4: Short chain  10:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.15953   
           Start-tree-ln(L)=ln P(D|G):                 -67.30171
           Pop. Theta    M
             1  5.66390 ------    3.2 
             2  4.41653    1.8 ------ 
 
           Maximization cycles needed: 39
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.13   |        0 ||
               1.5000  |   0.11   |        0  ||
               1.0000  |   0.14   |        0   |
[  2] 12:30:23   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:23   [NODE:2] Locus 4: Long chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.65053   
           Start-tree-ln(L)=ln P(D|G):                 -73.17869
           Pop. Theta    M
             1  7.11236 ------    3.4 
             2  5.42473    1.7 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.14   |        0 ||
               1.5000  |   0.11   |        0  ||
               1.0000  |   0.14   |        0   |
[  2] 12:30:23   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:24   [NODE:1] Locus 3: Long chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.18979   
           Start-tree-ln(L)=ln P(D|G):                 -22.69852
           Pop. Theta    M
             1  2.25127 ------    3.7 
             2  1.38212    7.0 ------ 
 
           Maximization cycles needed: 14
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.36   |        0 ||
               1.5000  |   0.28   |        0  ||
               1.0000  |   0.31   |        0   |
[  1] 12:30:24   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:24   [NODE:2] Locus 4: Long chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.41090   
           Start-tree-ln(L)=ln P(D|G):                 -67.53348
           Pop. Theta    M
             1  7.11305 ------    3.6 
             2  6.89735    2.0 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.14   |        0 ||
               1.5000  |   0.11   |        0  ||
               1.0000  |   0.14   |        0   |
[  2] 12:30:24   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:24   [NODE:1] Locus 3: Long chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.26429   
           Start-tree-ln(L)=ln P(D|G):                 -29.94332
           Pop. Theta    M
             1  2.86838 ------    4.3 
             2  1.74071    5.6 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.32   |        0 ||
               1.5000  |   0.28   |        0  ||
               1.0000  |   0.29   |        0   |
[  1] 12:30:24   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:25   [NODE:2] Locus 4: Long chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.23380   
           Start-tree-ln(L)=ln P(D|G):                 -64.09572
           Pop. Theta    M
             1  8.18566 ------    3.7 
             2  7.76126    2.2 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.13   |        0 ||
               1.5000  |   0.11   |        0  ||
               1.0000  |   0.14   |        0   |
           Prognosed end of sampling is    12:31 May 12 2010
12:30:25   Multiple chain estimates:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.46760   
           Pop. Theta    M
             1  8.18566 ------    3.7 
             2  7.76126    2.2 ------ 
 
           Maximization cycles needed: 39
           Norm of first derivatives:  0.000001


[  2] Locus 5  : Replicate 1
[  2] 12:30:25   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:25   [NODE:1] Locus 3: Long chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.72808   
           Start-tree-ln(L)=ln P(D|G):                 -34.72917
           Pop. Theta    M
             1  2.49695 ------    5.6 
             2  2.11366    6.9 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.33   |        0 ||
               1.5000  |   0.30   |        0  ||
               1.0000  |   0.32   |        0   |
           Prognosed end of sampling is    12:31 May 12 2010
12:30:25   Multiple chain estimates:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.45628   
           Pop. Theta    M
             1  2.49681 ------    5.6 
             2  2.11368    6.9 ------ 
 
           Maximization cycles needed: 7
           Norm of first derivatives:  0.000000


[  1] Locus 6  : Replicate 1
[  1] 12:30:25   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:25   [NODE:2] Locus 5: Short chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.37216   
           Start-tree-ln(L)=ln P(D|G):                 -17.41115
           Pop. Theta    M
             1  0.97180 ------    1.3 
             2  0.88534    2.8 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.49   |        0 ||
               1.5000  |   0.42   |        0  ||
               1.0000  |   0.39   |        0   |
[  2] 12:30:25   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:25   [NODE:1] Locus 6: Short chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.84079   
           Start-tree-ln(L)=ln P(D|G):                 -23.97189
           Pop. Theta    M
             1  1.33572 ------    1.5 
             2  0.95438    1.3 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.26   |        0 ||
               1.5000  |   0.24   |        0  ||
               1.0000  |   0.19   |        0   |
[  1] 12:30:25   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:25   [NODE:2] Locus 5: Short chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.54451   
           Start-tree-ln(L)=ln P(D|G):                 -13.62433
           Pop. Theta    M
             1  0.84597 ------    1.4 
             2  1.35682    2.9 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.48   |        0 ||
               1.5000  |   0.43   |        0  ||
               1.0000  |   0.37   |        0   |
[  2] 12:30:25   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:26   [NODE:1] Locus 6: Short chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.01098   
           Start-tree-ln(L)=ln P(D|G):                 -19.97059
           Pop. Theta    M
             1  1.35050 ------    2.1 
             2  1.07592    2.0 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.26   |        0 ||
               1.5000  |   0.24   |        0  ||
               1.0000  |   0.25   |        0   |
[  1] 12:30:26   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:26   [NODE:2] Locus 5: Short chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.85442   
           Start-tree-ln(L)=ln P(D|G):                 -14.59842
           Pop. Theta    M
             1  0.61824 ------    1.1 
             2  1.96300    2.7 ------ 
 
           Maximization cycles needed: 14
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.46   |        0 ||
               1.5000  |   0.40   |        0  ||
               1.0000  |   0.39   |        0   |
[  2] 12:30:26   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:26   [NODE:1] Locus 6: Short chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.80953   
           Start-tree-ln(L)=ln P(D|G):                 -24.26874
           Pop. Theta    M
             1  1.60832 ------    2.3 
             2  1.08615    2.9 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.26   |        0 ||
               1.5000  |   0.23   |        0  ||
               1.0000  |   0.27   |        0   |
[  1] 12:30:26   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:26   [NODE:2] Locus 5: Short chain   4:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.15191   
           Start-tree-ln(L)=ln P(D|G):                 -16.10784
           Pop. Theta    M
             1  0.58241 ------    0.0 
             2  2.39287    2.1 ------ 
 
           Maximization cycles needed: 23
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.50   |        0 ||
               1.5000  |   0.45   |        0  ||
               1.0000  |   0.41   |        0   |
[  2] 12:30:26   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:26   [NODE:1] Locus 6: Short chain   4:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.76432   
           Start-tree-ln(L)=ln P(D|G):                 -28.30180
           Pop. Theta    M
             1  1.89314 ------    3.0 
             2  1.17430    2.2 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.26   |        0 ||
               1.5000  |   0.21   |        0  ||
               1.0000  |   0.22   |        0   |
[  1] 12:30:26   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:26   [NODE:2] Locus 5: Short chain   5:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.47557   
           Start-tree-ln(L)=ln P(D|G):                 -16.24961
           Pop. Theta    M
             1  0.46690 ------    0.0 
             2  3.64758    2.4 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.45   |        0 ||
               1.5000  |   0.41   |        0  ||
               1.0000  |   0.41   |        0   |
[  2] 12:30:26   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:26   [NODE:1] Locus 6: Short chain   5:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.72669   
           Start-tree-ln(L)=ln P(D|G):                 -23.44660
           Pop. Theta    M
             1  1.74311 ------    3.5 
             2  1.43646    2.1 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.26   |        0 ||
               1.5000  |   0.21   |        0  ||
               1.0000  |   0.24   |        0   |
[  1] 12:30:26   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:27   [NODE:2] Locus 5: Short chain   6:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.71207   
           Start-tree-ln(L)=ln P(D|G):                 -21.82908
           Pop. Theta    M
             1  0.53794 ------    0.0 
             2  3.24311    2.8 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.49   |        0 ||
               1.5000  |   0.43   |        0  ||
               1.0000  |   0.41   |        0   |
[  2] 12:30:27   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:27   [NODE:1] Locus 6: Short chain   6:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.82242   
           Start-tree-ln(L)=ln P(D|G):                 -27.91554
           Pop. Theta    M
             1  1.99086 ------    3.4 
             2  1.24797    3.0 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.25   |        0 ||
               1.5000  |   0.23   |        0  ||
               1.0000  |   0.25   |        0   |
[  1] 12:30:27   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:27   [NODE:2] Locus 5: Short chain   7:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.75185   
           Start-tree-ln(L)=ln P(D|G):                 -18.31748
           Pop. Theta    M
             1  0.57637 ------    0.0 
             2  2.68127    3.9 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.49   |        0 ||
               1.5000  |   0.43   |        0  ||
               1.0000  |   0.40   |        0   |
[  2] 12:30:27   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:27   [NODE:1] Locus 6: Short chain   7:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.55420   
           Start-tree-ln(L)=ln P(D|G):                 -27.85671
           Pop. Theta    M
             1  1.83962 ------    3.1 
             2  1.25348    2.1 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.28   |        0 ||
               1.5000  |   0.25   |        0  ||
               1.0000  |   0.20   |        0   |
[  1] 12:30:27   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:27   [NODE:2] Locus 5: Short chain   8:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.40794   
           Start-tree-ln(L)=ln P(D|G):                 -21.37110
           Pop. Theta    M
             1  0.54598 ------    0.0 
             2  2.92793    7.5 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.47   |        0 ||
               1.5000  |   0.40   |        0  ||
               1.0000  |   0.40   |        0   |
[  2] 12:30:27   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:27   [NODE:1] Locus 6: Short chain   8:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.03998   
           Start-tree-ln(L)=ln P(D|G):                 -21.43286
           Pop. Theta    M
             1  1.64615 ------    3.8 
             2  1.61820    2.0 ------ 
 
           Maximization cycles needed: 8
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.23   |        0 ||
               1.5000  |   0.25   |        0  ||
               1.0000  |   0.23   |        0   |
[  1] 12:30:27   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:28   [NODE:2] Locus 5: Short chain   9:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.24080   
           Start-tree-ln(L)=ln P(D|G):                 -18.26851
           Pop. Theta    M
             1  0.71491 ------    0.0 
             2  1.74697    7.2 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.46   |        0 ||
               1.5000  |   0.42   |        0  ||
               1.0000  |   0.42   |        0   |
[  2] 12:30:28   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:28   [NODE:1] Locus 6: Short chain   9:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     6.01708   
           Start-tree-ln(L)=ln P(D|G):                 -43.16942
           Pop. Theta    M
             1  2.33320 ------    4.5 
             2  2.09844    1.1 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000001
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.26   |        0 ||
               1.5000  |   0.24   |        0  ||
               1.0000  |   0.23   |        0   |
[  1] 12:30:28   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:28   [NODE:2] Locus 5: Short chain  10:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.06276   
           Start-tree-ln(L)=ln P(D|G):                 -14.23953
           Pop. Theta    M
             1  0.65244 ------    0.0 
             2  1.69517    6.8 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.44   |        0 ||
               1.5000  |   0.41   |        0  ||
               1.0000  |   0.41   |        0   |
[  2] 12:30:28   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:28   [NODE:1] Locus 6: Short chain  10:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.04153   
           Start-tree-ln(L)=ln P(D|G):                 -30.74155
           Pop. Theta    M
             1  2.25142 ------    5.8 
             2  2.14231    1.2 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.24   |        0 ||
               1.5000  |   0.21   |        0  ||
               1.0000  |   0.23   |        0   |
[  1] 12:30:28   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:29   [NODE:2] Locus 5: Long chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.86995   
           Start-tree-ln(L)=ln P(D|G):                 -20.82042
           Pop. Theta    M
             1  0.48759 ------    0.0 
             2  1.33681    5.5 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.49   |        0 ||
               1.5000  |   0.43   |        0  ||
               1.0000  |   0.39   |        0   |
[  2] 12:30:29   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:29   [NODE:1] Locus 6: Long chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     4.15034   
           Start-tree-ln(L)=ln P(D|G):                 -36.63434
           Pop. Theta    M
             1  2.10956 ------    4.2 
             2  3.02114    0.9 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.26   |        0 ||
               1.5000  |   0.24   |        0  ||
               1.0000  |   0.21   |        0   |
[  1] 12:30:29   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:29   [NODE:2] Locus 5: Long chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     5.30174   
           Start-tree-ln(L)=ln P(D|G):                 -10.04088
           Pop. Theta    M
             1  0.70418 ------    0.0 
             2  1.76117    3.0 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.46   |        0 ||
               1.5000  |   0.42   |        0  ||
               1.0000  |   0.38   |        0   |
[  2] 12:30:29   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:29   [NODE:1] Locus 6: Long chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.03133   
           Start-tree-ln(L)=ln P(D|G):                 -36.13489
           Pop. Theta    M
             1  3.20650 ------    4.9 
             2  3.09996    1.1 ------ 
 
           Maximization cycles needed: 13
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.26   |        0 ||
               1.5000  |   0.24   |        0  ||
               1.0000  |   0.23   |        0   |
[  1] 12:30:29   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:30   [NODE:2] Locus 5: Long chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.65011   
           Start-tree-ln(L)=ln P(D|G):                 -11.24371
           Pop. Theta    M
             1  0.84086 ------    0.0 
             2  1.69210    4.2 ------ 
 
           Maximization cycles needed: 40
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.48   |        0 ||
               1.5000  |   0.42   |        0  ||
               1.0000  |   0.38   |        0   |


[  2] Locus 5  : Replicate 2
[  2] 12:30:30   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:30   [NODE:1] Locus 6: Long chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.13751   
           Start-tree-ln(L)=ln P(D|G):                 -42.10570
           Pop. Theta    M
             1  2.36853 ------    4.3 
             2  2.81052    1.2 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.25   |        0 ||
               1.5000  |   0.22   |        0  ||
               1.0000  |   0.24   |        0   |


[  1] Locus 6  : Replicate 2
[  1] 12:30:30   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:30   [NODE:2] Locus 5: Short chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     7.16515   
           Start-tree-ln(L)=ln P(D|G):                 -21.65302
           Pop. Theta    M
             1  1.36268 ------    1.4 
             2  1.22389    3.1 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.46   |        0 ||
               1.5000  |   0.43   |        0  ||
               1.0000  |   0.41   |        0   |
[  2] 12:30:30   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:30   [NODE:1] Locus 6: Short chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     8.09717   
           Start-tree-ln(L)=ln P(D|G):                 -26.29613
           Pop. Theta    M
             1  1.48628 ------    2.3 
             2  1.05232    1.4 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.28   |        0 ||
               1.5000  |   0.22   |        0  ||
               1.0000  |   0.25   |        0   |
[  1] 12:30:30   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:30   [NODE:2] Locus 5: Short chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.89551   
           Start-tree-ln(L)=ln P(D|G):                 -21.58659
           Pop. Theta    M
             1  1.66412 ------    1.6 
             2  1.49243    3.0 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.47   |        0 ||
               1.5000  |   0.43   |        0  ||
               1.0000  |   0.42   |        0   |
[  2] 12:30:30   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:30   [NODE:1] Locus 6: Short chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.30588   
           Start-tree-ln(L)=ln P(D|G):                 -24.89037
           Pop. Theta    M
             1  1.88089 ------    3.6 
             2  1.23603    1.6 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.27   |        0 ||
               1.5000  |   0.23   |        0  ||
               1.0000  |   0.23   |        0   |
[  1] 12:30:30   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:31   [NODE:1] Locus 6: Short chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.56754   
           Start-tree-ln(L)=ln P(D|G):                 -32.20300
           Pop. Theta    M
             1  2.10208 ------    2.6 
             2  1.41308    1.5 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.25   |        0 ||
               1.5000  |   0.24   |        0  ||
               1.0000  |   0.24   |        0   |
[  1] 12:30:31   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:31   [NODE:2] Locus 5: Short chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.68656   
           Start-tree-ln(L)=ln P(D|G):                 -17.31222
           Pop. Theta    M
             1  1.54093 ------    2.2 
             2  1.24263    4.4 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.49   |        0 ||
               1.5000  |   0.43   |        0  ||
               1.0000  |   0.39   |        0   |
[  2] 12:30:31   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:31   [NODE:1] Locus 6: Short chain   4:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.24624   
           Start-tree-ln(L)=ln P(D|G):                 -34.75543
           Pop. Theta    M
             1  2.63244 ------    2.2 
             2  1.59666    1.7 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
           Prognosed end of sampling is    12:31 May 12 2010
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.32   |        0 ||
               1.5000  |   0.27   |        0  ||
               1.0000  |   0.24   |        0   |
12:30:31   [NODE:2] Locus 5: Short chain   4:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.30456   
           Start-tree-ln(L)=ln P(D|G):                 -21.33802
           Pop. Theta    M
             1  1.55639 ------    1.0 
             2  1.51749    4.3 ------ 
 
[  1] 12:30:31   Burn-in (first 1000 trees are not used)
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.50   |        0 ||
               1.5000  |   0.42   |        0  ||
               1.0000  |   0.44   |        0   |
[  2] 12:30:31   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:31   [NODE:1] Locus 6: Short chain   5:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.58963   
           Start-tree-ln(L)=ln P(D|G):                 -45.21371
           Pop. Theta    M
             1  2.36990 ------    2.4 
             2  1.35924    2.3 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.30   |        0 ||
               1.5000  |   0.21   |        0  ||
               1.0000  |   0.24   |        0   |
[  1] 12:30:31   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:31   [NODE:2] Locus 5: Short chain   5:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.81173   
           Start-tree-ln(L)=ln P(D|G):                 -24.58971
           Pop. Theta    M
             1  1.67959 ------    0.6 
             2  1.15074    6.1 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.45   |        0 ||
               1.5000  |   0.41   |        0  ||
               1.0000  |   0.41   |        0   |
[  2] 12:30:31   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:32   [NODE:1] Locus 6: Short chain   6:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     4.33508   
           Start-tree-ln(L)=ln P(D|G):                 -32.11386
           Pop. Theta    M
             1  3.41044 ------    2.8 
             2  1.49066    3.1 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.27   |        0 ||
               1.5000  |   0.24   |        0  ||
               1.0000  |   0.24   |        0   |
[  1] 12:30:32   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:32   [NODE:2] Locus 5: Short chain   6:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.80248   
           Start-tree-ln(L)=ln P(D|G):                 -21.56679
           Pop. Theta    M
             1  1.47684 ------    0.6 
             2  1.54895    9.7 ------ 
 
           Maximization cycles needed: 13
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.50   |        0 ||
               1.5000  |   0.41   |        0  ||
               1.0000  |   0.42   |        0   |
[  2] 12:30:32   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:32   [NODE:1] Locus 6: Short chain   7:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.53974   
           Start-tree-ln(L)=ln P(D|G):                 -35.54923
           Pop. Theta    M
             1  3.55093 ------    2.8 
             2  1.26347    4.2 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.28   |        0 ||
               1.5000  |   0.21   |        0  ||
               1.0000  |   0.25   |        0   |
[  1] 12:30:32   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:32   [NODE:2] Locus 5: Short chain   7:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.46727   
           Start-tree-ln(L)=ln P(D|G):                 -16.44093
           Pop. Theta    M
             1  1.52692 ------    0.8 
             2  1.15851   15.2 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.50   |        0 ||
               1.5000  |   0.43   |        0  ||
               1.0000  |   0.42   |        0   |
[  2] 12:30:32   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:32   [NODE:1] Locus 6: Short chain   8:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.33832   
           Start-tree-ln(L)=ln P(D|G):                 -32.84834
           Pop. Theta    M
             1  4.30109 ------    2.8 
             2  1.46935    5.5 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.29   |        0 ||
               1.5000  |   0.24   |        0  ||
               1.0000  |   0.23   |        0   |
[  1] 12:30:32   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:33   [NODE:2] Locus 5: Short chain   8:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.90550   
           Start-tree-ln(L)=ln P(D|G):                 -19.27810
           Pop. Theta    M
             1  1.92322 ------    0.9 
             2  1.00527   13.8 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.50   |        0 ||
               1.5000  |   0.42   |        0  ||
               1.0000  |   0.42   |        0   |
[  2] 12:30:33   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:33   [NODE:1] Locus 6: Short chain   9:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     4.36843   
           Start-tree-ln(L)=ln P(D|G):                 -40.33779
           Pop. Theta    M
             1  3.21929 ------    2.3 
             2  1.51198    7.0 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.26   |        0 ||
               1.5000  |   0.25   |        0  ||
               1.0000  |   0.26   |        0   |
[  1] 12:30:33   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:33   [NODE:2] Locus 5: Short chain   9:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.42453   
           Start-tree-ln(L)=ln P(D|G):                 -16.93236
           Pop. Theta    M
             1  1.92052 ------    0.6 
             2  1.08690   15.2 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.48   |        0 ||
               1.5000  |   0.40   |        0  ||
               1.0000  |   0.40   |        0   |
[  2] 12:30:33   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:33   [NODE:1] Locus 6: Short chain  10:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.77681   
           Start-tree-ln(L)=ln P(D|G):                 -37.98625
           Pop. Theta    M
             1  3.44395 ------    1.9 
             2  0.84935    7.7 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.24   |        0 ||
               1.5000  |   0.22   |        0  ||
               1.0000  |   0.25   |        0   |
[  1] 12:30:33   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:33   [NODE:2] Locus 5: Short chain  10:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     4.22580   
           Start-tree-ln(L)=ln P(D|G):                 -20.79455
           Pop. Theta    M
             1  1.33317 ------    0.6 
             2  1.43008   11.7 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.44   |        0 ||
               1.5000  |   0.42   |        0  ||
               1.0000  |   0.40   |        0   |
[  2] 12:30:33   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:34   [NODE:1] Locus 6: Long chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.33395   
           Start-tree-ln(L)=ln P(D|G):                 -31.96436
           Pop. Theta    M
             1  3.51232 ------    2.5 
             2  0.67618    8.4 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.26   |        0 ||
               1.5000  |   0.23   |        0  ||
               1.0000  |   0.22   |        0   |
[  1] 12:30:34   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:34   [NODE:2] Locus 5: Long chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.04208   
           Start-tree-ln(L)=ln P(D|G):                 -17.22460
           Pop. Theta    M
             1  1.86588 ------    1.0 
             2  1.23775   10.0 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.45   |        0 ||
               1.5000  |   0.40   |        0  ||
               1.0000  |   0.43   |        0   |
[  2] 12:30:34   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:35   [NODE:1] Locus 6: Long chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.25650   
           Start-tree-ln(L)=ln P(D|G):                 -35.02798
           Pop. Theta    M
             1  3.63502 ------    2.4 
             2  0.75433    6.2 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.26   |        0 ||
               1.5000  |   0.22   |        0  ||
               1.0000  |   0.23   |        0   |
[  1] 12:30:35   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:35   [NODE:2] Locus 5: Long chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.73899   
           Start-tree-ln(L)=ln P(D|G):                 -15.75029
           Pop. Theta    M
             1  1.42197 ------    0.5 
             2  0.89908   11.9 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.49   |        0 ||
               1.5000  |   0.43   |        0  ||
               1.0000  |   0.39   |        0   |
[  2] 12:30:35   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:35   [NODE:1] Locus 6: Long chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.65578   
           Start-tree-ln(L)=ln P(D|G):                 -28.44640
           Pop. Theta    M
             1  5.27992 ------    2.3 
             2  0.76901    6.3 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.26   |        0 ||
               1.5000  |   0.23   |        0  ||
               1.0000  |   0.24   |        0   |
           Prognosed end of sampling is    12:31 May 12 2010
12:30:35   Multiple chain estimates:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.31155   
           Pop. Theta    M
             1  5.27992 ------    2.3 
             2  0.76901    6.3 ------ 
 
           Maximization cycles needed: 0
           Norm of first derivatives:  0.000000


[  1] Locus 7  : Replicate 1
[  1] 12:30:35   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:35   [NODE:2] Locus 5: Long chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.83482   
           Start-tree-ln(L)=ln P(D|G):                 -23.41385
           Pop. Theta    M
             1  1.58626 ------    0.5 
             2  0.46596   12.7 ------ 
 
           Maximization cycles needed: 14
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.48   |        0 ||
               1.5000  |   0.43   |        0  ||
               1.0000  |   0.41   |        0   |
           Prognosed end of sampling is    12:31 May 12 2010
12:30:35   Multiple chain estimates:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     5.66964   
           Pop. Theta    M
             1  1.58626 ------    0.5 
             2  0.46596   12.7 ------ 
 
           Maximization cycles needed: 0
           Norm of first derivatives:  0.000000


[  2] Locus 8  : Replicate 1
[  2] 12:30:35   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:35   [NODE:1] Locus 7: Short chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     6.68245   
           Start-tree-ln(L)=ln P(D|G):                 -14.08762
           Pop. Theta    M
             1  0.88970 ------    1.9 
             2  1.46405    2.1 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.46   |        0 ||
               1.5000  |   0.41   |        0  ||
               1.0000  |   0.36   |        0   |
[  1] 12:30:35   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:36   [NODE:2] Locus 8: Short chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     7.06894   
           Start-tree-ln(L)=ln P(D|G):                 -18.84139
           Pop. Theta    M
             1  1.37423 ------    1.7 
             2  1.17344    2.0 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.33   |        0 ||
               1.5000  |   0.24   |        0  ||
               1.0000  |   0.28   |        0   |
[  2] 12:30:36   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:36   [NODE:1] Locus 7: Short chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.09464   
           Start-tree-ln(L)=ln P(D|G):                 -19.56785
           Pop. Theta    M
             1  0.78787 ------    2.4 
             2  1.33939    1.3 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.42   |        0 ||
               1.5000  |   0.38   |        0  ||
               1.0000  |   0.35   |        0   |
[  1] 12:30:36   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:36   [NODE:2] Locus 8: Short chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.61955   
           Start-tree-ln(L)=ln P(D|G):                 -30.82328
           Pop. Theta    M
             1  1.53792 ------    1.7 
             2  1.34430    2.3 ------ 
 
           Maximization cycles needed: 8
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.34   |        0 ||
               1.5000  |   0.30   |        0  ||
               1.0000  |   0.31   |        0   |
[  2] 12:30:36   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:36   [NODE:1] Locus 7: Short chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.26288   
           Start-tree-ln(L)=ln P(D|G):                 -16.36667
           Pop. Theta    M
             1  0.87077 ------    2.7 
             2  1.64903    1.1 ------ 
 
           Maximization cycles needed: 8
           Norm of first derivatives:  0.000001
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.39   |        0 ||
               1.5000  |   0.40   |        0  ||
               1.0000  |   0.35   |        0   |
[  1] 12:30:36   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:36   [NODE:2] Locus 8: Short chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.44009   
           Start-tree-ln(L)=ln P(D|G):                 -31.36279
           Pop. Theta    M
             1  1.36268 ------    1.5 
             2  1.60843    2.3 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.36   |        0 ||
               1.5000  |   0.28   |        0  ||
               1.0000  |   0.27   |        0   |
[  2] 12:30:36   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:37   [NODE:1] Locus 7: Short chain   4:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.50488   
           Start-tree-ln(L)=ln P(D|G):                 -15.82201
           Pop. Theta    M
             1  0.76361 ------    5.2 
             2  1.49303    1.3 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.40   |        0 ||
               1.5000  |   0.34   |        0  ||
               1.0000  |   0.38   |        0   |
[  1] 12:30:37   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:37   [NODE:2] Locus 8: Short chain   4:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.38049   
           Start-tree-ln(L)=ln P(D|G):                 -36.85987
           Pop. Theta    M
             1  1.44716 ------    1.9 
             2  1.89418    1.5 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.37   |        0 ||
               1.5000  |   0.30   |        0  ||
               1.0000  |   0.27   |        0   |
[  2] 12:30:37   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
           Prognosed end of sampling is    12:31 May 12 2010
12:30:37   [NODE:1] Locus 7: Short chain   5:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.82109   
           Start-tree-ln(L)=ln P(D|G):                 -15.58482
           Pop. Theta    M
             1  0.89347 ------    4.9 
             2  1.40896    2.4 ------ 
 
12:30:37   [NODE:2] Locus 8: Short chain   5:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.81178   
           Start-tree-ln(L)=ln P(D|G):                 -24.29667
           Pop. Theta    M
             1  1.74746 ------    2.2 
             2  1.90358    1.4 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
           Maximization cycles needed: 8
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.39   |        0 ||
               1.5000  |   0.37   |        0  ||
               1.0000  |   0.39   |        0   |
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.38   |        0 ||
               1.5000  |   0.27   |        0  ||
               1.0000  |   0.32   |        0   |
[  1] 12:30:37   Burn-in (first 1000 trees are not used)
[  2] 12:30:37   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:37   [NODE:2] Locus 8: Short chain   6:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.90447   
           Start-tree-ln(L)=ln P(D|G):                 -35.38201
           Pop. Theta    M
             1  1.76078 ------    3.4 
             2  2.66262    1.4 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.37   |        0 ||
               1.5000  |   0.27   |        0  ||
               1.0000  |   0.32   |        0   |
[  2] 12:30:37   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:37   [NODE:1] Locus 7: Short chain   6:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.56163   
           Start-tree-ln(L)=ln P(D|G):                 -22.10762
           Pop. Theta    M
             1  1.11699 ------    5.0 
             2  2.16806    2.5 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.36   |        0 ||
               1.5000  |   0.35   |        0  ||
               1.0000  |   0.35   |        0   |
[  1] 12:30:37   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:38   [NODE:2] Locus 8: Short chain   7:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.53199   
           Start-tree-ln(L)=ln P(D|G):                 -36.40213
           Pop. Theta    M
             1  1.86672 ------    2.2 
             2  2.65216    1.0 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.40   |        0 ||
               1.5000  |   0.32   |        0  ||
               1.0000  |   0.28   |        0   |
[  2] 12:30:38   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:38   [NODE:1] Locus 7: Short chain   7:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.88155   
           Start-tree-ln(L)=ln P(D|G):                 -28.02990
           Pop. Theta    M
             1  1.03647 ------    3.5 
             2  1.82887    1.8 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.38   |        0 ||
               1.5000  |   0.38   |        0  ||
               1.0000  |   0.37   |        0   |
[  1] 12:30:38   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:38   [NODE:2] Locus 8: Short chain   8:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.88152   
           Start-tree-ln(L)=ln P(D|G):                 -40.68383
           Pop. Theta    M
             1  1.55829 ------    1.9 
             2  3.64294    0.8 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.38   |        0 ||
               1.5000  |   0.28   |        0  ||
               1.0000  |   0.31   |        0   |
[  2] 12:30:38   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:38   [NODE:1] Locus 7: Short chain   8:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.11560   
           Start-tree-ln(L)=ln P(D|G):                 -24.01626
           Pop. Theta    M
             1  0.96485 ------    3.3 
             2  1.42039    1.4 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.42   |        0 ||
               1.5000  |   0.42   |        0  ||
               1.0000  |   0.38   |        0   |
[  1] 12:30:38   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:38   [NODE:2] Locus 8: Short chain   9:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.08952   
           Start-tree-ln(L)=ln P(D|G):                 -42.88292
           Pop. Theta    M
             1  1.59939 ------    1.6 
             2  3.90298    1.3 ------ 
 
           Maximization cycles needed: 13
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.36   |        0 ||
               1.5000  |   0.29   |        0  ||
               1.0000  |   0.32   |        0   |
[  2] 12:30:38   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:38   [NODE:1] Locus 7: Short chain   9:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.20161   
           Start-tree-ln(L)=ln P(D|G):                 -20.09662
           Pop. Theta    M
             1  0.79834 ------    4.1 
             2  1.99092    1.8 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000001
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.39   |        0 ||
               1.5000  |   0.38   |        0  ||
               1.0000  |   0.37   |        0   |
[  1] 12:30:38   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:38   [NODE:2] Locus 8: Short chain  10:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.70779   
           Start-tree-ln(L)=ln P(D|G):                 -44.79283
           Pop. Theta    M
             1  1.96043 ------    1.7 
             2  3.97446    1.7 ------ 
 
           Maximization cycles needed: 21
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.37   |        0 ||
               1.5000  |   0.26   |        0  ||
               1.0000  |   0.34   |        0   |
[  2] 12:30:38   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:39   [NODE:1] Locus 7: Short chain  10:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.51352   
           Start-tree-ln(L)=ln P(D|G):                 -17.60528
           Pop. Theta    M
             1  0.64450 ------    5.5 
             2  2.02517    2.0 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.41   |        0 ||
               1.5000  |   0.39   |        0  ||
               1.0000  |   0.36   |        0   |
[  1] 12:30:39   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:39   [NODE:1] Locus 7: Long chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.38231   
           Start-tree-ln(L)=ln P(D|G):                 -20.30076
           Pop. Theta    M
             1  0.74924 ------    7.4 
             2  2.33271    2.3 ------ 
 
           Maximization cycles needed: 13
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.37   |        0 ||
               1.5000  |   0.40   |        0  ||
               1.0000  |   0.36   |        0   |
[  1] 12:30:39   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:39   [NODE:2] Locus 8: Long chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.00314   
           Start-tree-ln(L)=ln P(D|G):                 -39.24065
           Pop. Theta    M
             1  1.83730 ------    1.7 
             2  3.40805    0.8 ------ 
 
           Maximization cycles needed: 13
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.33   |        0 ||
               1.5000  |   0.28   |        0  ||
               1.0000  |   0.33   |        0   |
[  2] 12:30:39   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:40   [NODE:1] Locus 7: Long chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.95957   
           Start-tree-ln(L)=ln P(D|G):                 -29.77655
           Pop. Theta    M
             1  0.97010 ------    7.6 
             2  2.57318    1.5 ------ 
 
           Maximization cycles needed: 13
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.38   |        0 ||
               1.5000  |   0.37   |        0  ||
               1.0000  |   0.36   |        0   |
[  1] 12:30:40   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:40   [NODE:2] Locus 8: Long chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.78519   
           Start-tree-ln(L)=ln P(D|G):                 -30.82361
           Pop. Theta    M
             1  1.95683 ------    3.7 
             2  3.09836    0.7 ------ 
 
           Maximization cycles needed: 13
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.35   |        0 ||
               1.5000  |   0.28   |        0  ||
               1.0000  |   0.36   |        0   |
[  2] 12:30:40   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:40   [NODE:1] Locus 7: Long chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.52021   
           Start-tree-ln(L)=ln P(D|G):                 -18.39781
           Pop. Theta    M
             1  0.94335 ------    5.7 
             2  2.25278    1.3 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.37   |        0 ||
               1.5000  |   0.36   |        0  ||
               1.0000  |   0.36   |        0   |


[  1] Locus 7  : Replicate 2
[  1] 12:30:41   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:41   [NODE:2] Locus 8: Long chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.00012   
           Start-tree-ln(L)=ln P(D|G):                 -33.66091
           Pop. Theta    M
             1  1.39430 ------    3.9 
             2  3.14605    0.5 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.35   |        0 ||
               1.5000  |   0.30   |        0  ||
               1.0000  |   0.33   |        0   |


[  2] Locus 8  : Replicate 2
[  2] 12:30:41   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:41   [NODE:1] Locus 7: Short chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     7.55698   
           Start-tree-ln(L)=ln P(D|G):                 -20.11677
           Pop. Theta    M
             1  0.85046 ------    2.9 
             2  1.33216    1.9 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.41   |        0 ||
               1.5000  |   0.39   |        0  ||
               1.0000  |   0.37   |        0   |
[  1] 12:30:41   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:41   [NODE:2] Locus 8: Short chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     5.35353   
           Start-tree-ln(L)=ln P(D|G):                 -34.98669
           Pop. Theta    M
             1  0.94229 ------    1.9 
             2  1.15261    2.4 ------ 
 
           Maximization cycles needed: 13
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.32   |        0 ||
               1.5000  |   0.29   |        0  ||
               1.0000  |   0.29   |        0   |
[  2] 12:30:41   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
           Prognosed end of sampling is    12:31 May 12 2010
12:30:41   [NODE:1] Locus 7: Short chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.10390   
           Start-tree-ln(L)=ln P(D|G):                 -14.22137
           Pop. Theta    M
             1  0.66523 ------    2.8 
             2  1.80824    2.3 ------ 
 
12:30:41   [NODE:2] Locus 8: Short chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.90369   
           Start-tree-ln(L)=ln P(D|G):                 -31.06868
           Pop. Theta    M
             1  1.14248 ------    1.8 
             2  1.61620    1.7 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.43   |        0 ||
               1.5000  |   0.39   |        0  ||
               1.0000  |   0.36   |        0   |
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.33   |        0 ||
               1.5000  |   0.31   |        0  ||
               1.0000  |   0.33   |        0   |
[  1] 12:30:41   Burn-in (first 1000 trees are not used)
[  2] 12:30:41   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:42   [NODE:1] Locus 7: Short chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.75615   
           Start-tree-ln(L)=ln P(D|G):                 -16.56067
           Pop. Theta    M
             1  0.81685 ------    2.1 
             2  1.75797    2.9 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.42   |        0 ||
               1.5000  |   0.39   |        0  ||
               1.0000  |   0.35   |        0   |
[  1] 12:30:42   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:42   [NODE:2] Locus 8: Short chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.32180   
           Start-tree-ln(L)=ln P(D|G):                 -31.42081
           Pop. Theta    M
             1  1.72947 ------    1.8 
             2  1.80402    1.8 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.33   |        0 ||
               1.5000  |   0.28   |        0  ||
               1.0000  |   0.33   |        0   |
[  2] 12:30:42   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:42   [NODE:1] Locus 7: Short chain   4:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.92036   
           Start-tree-ln(L)=ln P(D|G):                 -21.39502
           Pop. Theta    M
             1  0.60286 ------    2.2 
             2  2.24755    2.1 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.43   |        0 ||
               1.5000  |   0.37   |        0  ||
               1.0000  |   0.39   |        0   |
[  1] 12:30:42   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:42   [NODE:2] Locus 8: Short chain   4:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.81513   
           Start-tree-ln(L)=ln P(D|G):                 -33.53128
           Pop. Theta    M
             1  1.97703 ------    1.7 
             2  1.71618    2.4 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.36   |        0 ||
               1.5000  |   0.31   |        0  ||
               1.0000  |   0.32   |        0   |
[  2] 12:30:42   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:42   [NODE:1] Locus 7: Short chain   5:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.98731   
           Start-tree-ln(L)=ln P(D|G):                 -21.76305
           Pop. Theta    M
             1  0.47154 ------    3.9 
             2  1.81415    2.0 ------ 
 
           Maximization cycles needed: 14
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.40   |        0 ||
               1.5000  |   0.37   |        0  ||
               1.0000  |   0.42   |        0   |
[  1] 12:30:42   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:42   [NODE:2] Locus 8: Short chain   5:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     7.94348   
           Start-tree-ln(L)=ln P(D|G):                 -37.05269
           Pop. Theta    M
             1  3.08392 ------    2.3 
             2  1.67368    0.8 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.37   |        0 ||
               1.5000  |   0.30   |        0  ||
               1.0000  |   0.31   |        0   |
[  2] 12:30:42   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:43   [NODE:1] Locus 7: Short chain   6:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.64770   
           Start-tree-ln(L)=ln P(D|G):                 -19.25320
           Pop. Theta    M
             1  0.42642 ------    4.5 
             2  2.11714    1.8 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.42   |        0 ||
               1.5000  |   0.35   |        0  ||
               1.0000  |   0.38   |        0   |
[  1] 12:30:43   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:43   [NODE:2] Locus 8: Short chain   6:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     5.67736   
           Start-tree-ln(L)=ln P(D|G):                 -25.99853
           Pop. Theta    M
             1  3.20317 ------    2.0 
             2  2.81284    1.0 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.36   |        0 ||
               1.5000  |   0.29   |        0  ||
               1.0000  |   0.28   |        0   |
[  2] 12:30:43   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
           Prognosed end of sampling is    12:31 May 12 2010
12:30:43   [NODE:1] Locus 7: Short chain   7:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.00732   
           Start-tree-ln(L)=ln P(D|G):                 -18.34567
           Pop. Theta    M
             1  0.46671 ------    4.0 
             2  2.27815    1.2 ------ 
 
12:30:43   [NODE:2] Locus 8: Short chain   7:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.11278   
           Start-tree-ln(L)=ln P(D|G):                 -37.81044
           Pop. Theta    M
             1  3.94288 ------    2.1 
             2  2.65264    1.3 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000001
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.41   |        0 ||
               1.5000  |   0.38   |        0  ||
               1.0000  |   0.36   |        0   |
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.35   |        0 ||
               1.5000  |   0.31   |        0  ||
               1.0000  |   0.32   |        0   |
[  1] 12:30:43   Burn-in (first 1000 trees are not used)
[  2] 12:30:43   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:43   [NODE:2] Locus 8: Short chain   8:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.38287   
           Start-tree-ln(L)=ln P(D|G):                 -46.99940
           Pop. Theta    M
             1  3.82689 ------    2.7 
             2  2.57342    1.6 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.34   |        0 ||
               1.5000  |   0.30   |        0  ||
               1.0000  |   0.32   |        0   |
[  2] 12:30:43   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:43   [NODE:1] Locus 7: Short chain   8:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.38364   
           Start-tree-ln(L)=ln P(D|G):                 -17.76266
           Pop. Theta    M
             1  0.62775 ------    4.0 
             2  2.54209    1.4 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.39   |        0 ||
               1.5000  |   0.36   |        0  ||
               1.0000  |   0.36   |        0   |
[  1] 12:30:43   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:44   [NODE:2] Locus 8: Short chain   9:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.21746   
           Start-tree-ln(L)=ln P(D|G):                 -38.06196
           Pop. Theta    M
             1  3.78154 ------    3.0 
             2  2.32404    1.7 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.35   |        0 ||
               1.5000  |   0.31   |        0  ||
               1.0000  |   0.34   |        0   |
[  2] 12:30:44   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:44   [NODE:1] Locus 7: Short chain   9:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     4.29287   
           Start-tree-ln(L)=ln P(D|G):                 -24.57330
           Pop. Theta    M
             1  0.57550 ------    7.4 
             2  3.03492    1.0 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.43   |        0 ||
               1.5000  |   0.35   |        0  ||
               1.0000  |   0.35   |        0   |
[  1] 12:30:44   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:44   [NODE:2] Locus 8: Short chain  10:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     5.61121   
           Start-tree-ln(L)=ln P(D|G):                 -42.25504
           Pop. Theta    M
             1  4.47621 ------    1.8 
             2  2.75798    1.6 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.36   |        0 ||
               1.5000  |   0.30   |        0  ||
               1.0000  |   0.37   |        0   |
[  2] 12:30:44   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:44   [NODE:1] Locus 7: Short chain  10:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.65423   
           Start-tree-ln(L)=ln P(D|G):                 -26.52485
           Pop. Theta    M
             1  0.75472 ------    5.6 
             2  3.61420    1.3 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.42   |        0 ||
               1.5000  |   0.39   |        0  ||
               1.0000  |   0.36   |        0   |
[  1] 12:30:44   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:45   [NODE:2] Locus 8: Long chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.55599   
           Start-tree-ln(L)=ln P(D|G):                 -47.63345
           Pop. Theta    M
             1  4.51964 ------    1.7 
             2  3.45479    2.1 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.33   |        0 ||
               1.5000  |   0.28   |        0  ||
               1.0000  |   0.33   |        0   |
[  2] 12:30:45   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:45   [NODE:1] Locus 7: Long chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.77331   
           Start-tree-ln(L)=ln P(D|G):                 -28.45751
           Pop. Theta    M
             1  0.70312 ------    5.2 
             2  3.69384    0.6 ------ 
 
           Maximization cycles needed: 19
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.41   |        0 ||
               1.5000  |   0.37   |        0  ||
               1.0000  |   0.36   |        0   |
[  1] 12:30:45   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
           Prognosed end of sampling is    12:31 May 12 2010
12:30:46   [NODE:1] Locus 7: Long chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.20712   
           Start-tree-ln(L)=ln P(D|G):                 -36.25076
           Pop. Theta    M
             1  0.94529 ------    4.4 
             2  4.04175    0.4 ------ 
 
12:30:46   [NODE:2] Locus 8: Long chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.73879   
           Start-tree-ln(L)=ln P(D|G):                 -43.23929
           Pop. Theta    M
             1  3.37886 ------    2.3 
             2  2.90301    1.6 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.40   |        0 ||
               1.5000  |   0.35   |        0  ||
               1.0000  |   0.39   |        0   |
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.34   |        0 ||
               1.5000  |   0.31   |        0  ||
               1.0000  |   0.35   |        0   |
[  1] 12:30:46   Burn-in (first 1000 trees are not used)
[  2] 12:30:46   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:46   [NODE:2] Locus 8: Long chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.42299   
           Start-tree-ln(L)=ln P(D|G):                 -44.54756
           Pop. Theta    M
             1  3.84855 ------    2.3 
             2  3.91206    1.7 ------ 
 
           Maximization cycles needed: 13
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.35   |        0 ||
               1.5000  |   0.29   |        0  ||
               1.0000  |   0.35   |        0   |
           Prognosed end of sampling is    12:31 May 12 2010
12:30:46   Multiple chain estimates:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.84599   
           Pop. Theta    M
             1  3.84855 ------    2.3 
             2  3.91206    1.7 ------ 
 
           Maximization cycles needed: 0
           Norm of first derivatives:  0.000001


[  2] Locus 9  : Replicate 1
[  2] 12:30:46   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:46   [NODE:1] Locus 7: Long chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.26843   
           Start-tree-ln(L)=ln P(D|G):                 -34.46949
           Pop. Theta    M
             1  0.64395 ------    3.9 
             2  3.55845    0.5 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.40   |        0 ||
               1.5000  |   0.37   |        0  ||
               1.0000  |   0.38   |        0   |
           Prognosed end of sampling is    12:31 May 12 2010
12:30:46   Multiple chain estimates:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.53681   
           Pop. Theta    M
             1  0.64395 ------    3.9 
             2  3.55846    0.5 ------ 
 
           Maximization cycles needed: 6
           Norm of first derivatives:  0.000001


[  1] Locus 10 : Replicate 1
[  1] 12:30:46   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:46   [NODE:2] Locus 9: Short chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     8.87973   
           Start-tree-ln(L)=ln P(D|G):                 -25.12400
           Pop. Theta    M
             1  1.45421 ------    1.9 
             2  0.93073    2.5 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.24   |        0 ||
               1.5000  |   0.22   |        0  ||
               1.0000  |   0.21   |        0   |
[  2] 12:30:46   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:47   [NODE:1] Locus 10: Short chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     5.01642   
           Start-tree-ln(L)=ln P(D|G):                 -31.17468
           Pop. Theta    M
             1  1.12739 ------    1.5 
             2  1.32782    1.7 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.23   |        0 ||
               1.5000  |   0.17   |        0  ||
               1.0000  |   0.21   |        0   |
[  1] 12:30:47   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:47   [NODE:2] Locus 9: Short chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.19412   
           Start-tree-ln(L)=ln P(D|G):                 -26.52923
           Pop. Theta    M
             1  1.62114 ------    1.8 
             2  1.05613    3.4 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.25   |        0 ||
               1.5000  |   0.22   |        0  ||
               1.0000  |   0.23   |        0   |
[  2] 12:30:47   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:47   [NODE:1] Locus 10: Short chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.90289   
           Start-tree-ln(L)=ln P(D|G):                 -36.42360
           Pop. Theta    M
             1  1.30746 ------    1.7 
             2  1.13235    1.1 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000001
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.23   |        0 ||
               1.5000  |   0.18   |        0  ||
               1.0000  |   0.20   |        0   |
[  1] 12:30:47   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:47   [NODE:2] Locus 9: Short chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     4.90857   
           Start-tree-ln(L)=ln P(D|G):                 -25.35162
           Pop. Theta    M
             1  2.01695 ------    1.6 
             2  1.62203    4.5 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.25   |        0 ||
               1.5000  |   0.23   |        0  ||
               1.0000  |   0.22   |        0   |
[  2] 12:30:47   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:47   [NODE:1] Locus 10: Short chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.09460   
           Start-tree-ln(L)=ln P(D|G):                 -41.41655
           Pop. Theta    M
             1  1.74124 ------    2.2 
             2  1.19821    1.4 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.27   |        0 ||
               1.5000  |   0.21   |        0  ||
               1.0000  |   0.19   |        0   |
[  1] 12:30:47   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:47   [NODE:2] Locus 9: Short chain   4:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.82454   
           Start-tree-ln(L)=ln P(D|G):                 -29.95634
           Pop. Theta    M
             1  2.53042 ------    2.3 
             2  1.74509    3.9 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.27   |        0 ||
               1.5000  |   0.23   |        0  ||
               1.0000  |   0.25   |        0   |
[  2] 12:30:47   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:47   [NODE:1] Locus 10: Short chain   4:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.24483   
           Start-tree-ln(L)=ln P(D|G):                 -44.16657
           Pop. Theta    M
             1  1.72119 ------    2.1 
             2  1.68481    1.4 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.25   |        0 ||
               1.5000  |   0.21   |        0  ||
               1.0000  |   0.23   |        0   |
[  1] 12:30:47   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:48   [NODE:2] Locus 9: Short chain   5:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.96210   
           Start-tree-ln(L)=ln P(D|G):                 -41.53122
           Pop. Theta    M
             1  2.99765 ------    1.9 
             2  2.50590    3.8 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.27   |        0 ||
               1.5000  |   0.24   |        0  ||
               1.0000  |   0.24   |        0   |
[  2] 12:30:48   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:48   [NODE:1] Locus 10: Short chain   5:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.40732   
           Start-tree-ln(L)=ln P(D|G):                 -55.64930
           Pop. Theta    M
             1  2.34064 ------    2.2 
             2  2.27081    1.4 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.23   |        0 ||
               1.5000  |   0.22   |        0  ||
               1.0000  |   0.18   |        0   |
[  1] 12:30:48   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:48   [NODE:2] Locus 9: Short chain   6:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.89134   
           Start-tree-ln(L)=ln P(D|G):                 -35.80463
           Pop. Theta    M
             1  3.22043 ------    2.3 
             2  2.61774    3.8 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.27   |        0 ||
               1.5000  |   0.22   |        0  ||
               1.0000  |   0.23   |        0   |
[  2] 12:30:48   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:48   [NODE:1] Locus 10: Short chain   6:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.83153   
           Start-tree-ln(L)=ln P(D|G):                 -48.65038
           Pop. Theta    M
             1  2.29663 ------    2.4 
             2  2.72886    1.3 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.23   |        0 ||
               1.5000  |   0.20   |        0  ||
               1.0000  |   0.23   |        0   |
[  1] 12:30:48   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:49   [NODE:2] Locus 9: Short chain   7:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.75682   
           Start-tree-ln(L)=ln P(D|G):                 -39.89204
           Pop. Theta    M
             1  3.47678 ------    2.5 
             2  2.18952    3.5 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.29   |        0 ||
               1.5000  |   0.24   |        0  ||
               1.0000  |   0.28   |        0   |
[  2] 12:30:49   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:49   [NODE:1] Locus 10: Short chain   7:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.13963   
           Start-tree-ln(L)=ln P(D|G):                 -46.58157
           Pop. Theta    M
             1  3.05418 ------    2.0 
             2  3.53975    1.6 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.21   |        0 ||
               1.5000  |   0.21   |        0  ||
               1.0000  |   0.22   |        0   |
[  1] 12:30:49   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:49   [NODE:2] Locus 9: Short chain   8:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.15898   
           Start-tree-ln(L)=ln P(D|G):                 -33.02232
           Pop. Theta    M
             1  2.90096 ------    2.7 
             2  2.61057    3.8 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.27   |        0 ||
               1.5000  |   0.23   |        0  ||
               1.0000  |   0.25   |        0   |
[  2] 12:30:49   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:49   [NODE:1] Locus 10: Short chain   8:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.40617   
           Start-tree-ln(L)=ln P(D|G):                 -44.70752
           Pop. Theta    M
             1  3.09936 ------    2.1 
             2  3.44504    1.3 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.21   |        0 ||
               1.5000  |   0.21   |        0  ||
               1.0000  |   0.20   |        0   |
[  1] 12:30:49   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
           Prognosed end of sampling is    12:31 May 12 2010
12:30:49   [NODE:1] Locus 10: Short chain   9:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.34917   
           Start-tree-ln(L)=ln P(D|G):                 -44.25461
           Pop. Theta    M
             1  3.53694 ------    2.4 
             2  4.88672    1.4 ------ 
 
12:30:49   [NODE:2] Locus 9: Short chain   9:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.42727   
           Start-tree-ln(L)=ln P(D|G):                 -47.79915
           Pop. Theta    M
             1  3.03634 ------    2.4 
             2  3.75711    3.8 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.23   |        0 ||
               1.5000  |   0.20   |        0  ||
               1.0000  |   0.20   |        0   |
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.29   |        0 ||
               1.5000  |   0.21   |        0  ||
               1.0000  |   0.24   |        0   |
[  1] 12:30:49   Burn-in (first 1000 trees are not used)
[  2] 12:30:49   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:50   [NODE:1] Locus 10: Short chain  10:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.70591   
           Start-tree-ln(L)=ln P(D|G):                 -45.78731
           Pop. Theta    M
             1  4.24703 ------    3.4 
             2  6.07848    1.3 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000001
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.22   |        0 ||
               1.5000  |   0.20   |        0  ||
               1.0000  |   0.26   |        0   |
[  1] 12:30:50   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:50   [NODE:2] Locus 9: Short chain  10:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.11717   
           Start-tree-ln(L)=ln P(D|G):                 -42.41969
           Pop. Theta    M
             1  3.75150 ------    2.1 
             2  3.52829    3.0 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.28   |        0 ||
               1.5000  |   0.23   |        0  ||
               1.0000  |   0.24   |        0   |
[  2] 12:30:50   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:50   [NODE:1] Locus 10: Long chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.41034   
           Start-tree-ln(L)=ln P(D|G):                 -66.82922
           Pop. Theta    M
             1  3.54206 ------    3.3 
             2  5.58473    1.3 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.24   |        0 ||
               1.5000  |   0.19   |        0  ||
               1.0000  |   0.25   |        0   |
[  1] 12:30:50   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:50   [NODE:2] Locus 9: Long chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.65286   
           Start-tree-ln(L)=ln P(D|G):                 -44.04645
           Pop. Theta    M
             1  3.69849 ------    2.6 
             2  5.38415    3.2 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.29   |        0 ||
               1.5000  |   0.24   |        0  ||
               1.0000  |   0.28   |        0   |
[  2] 12:30:50   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:51   [NODE:1] Locus 10: Long chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.69344   
           Start-tree-ln(L)=ln P(D|G):                 -59.48490
           Pop. Theta    M
             1  3.83738 ------    2.7 
             2  5.01961    1.3 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000001
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.23   |        0 ||
               1.5000  |   0.18   |        0  ||
               1.0000  |   0.23   |        0   |
[  1] 12:30:51   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:51   [NODE:2] Locus 9: Long chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.38495   
           Start-tree-ln(L)=ln P(D|G):                 -63.89042
           Pop. Theta    M
             1  3.92367 ------    2.3 
             2  6.21049    3.0 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.27   |        0 ||
               1.5000  |   0.24   |        0  ||
               1.0000  |   0.26   |        0   |
[  2] 12:30:51   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:51   [NODE:1] Locus 10: Long chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.67359   
           Start-tree-ln(L)=ln P(D|G):                 -60.85291
           Pop. Theta    M
             1  3.86562 ------    2.8 
             2  6.67690    1.7 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.24   |        0 ||
               1.5000  |   0.17   |        0  ||
               1.0000  |   0.24   |        0   |


[  1] Locus 10 : Replicate 2
[  1] 12:30:51   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:52   [NODE:2] Locus 9: Long chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.86247   
           Start-tree-ln(L)=ln P(D|G):                 -57.67015
           Pop. Theta    M
             1  3.18479 ------    3.1 
             2  8.24851    2.6 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.27   |        0 ||
               1.5000  |   0.24   |        0  ||
               1.0000  |   0.27   |        0   |


[  2] Locus 9  : Replicate 2
[  2] 12:30:52   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:52   [NODE:1] Locus 10: Short chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     10.71258  
           Start-tree-ln(L)=ln P(D|G):                 -32.47885
           Pop. Theta    M
             1  1.20031 ------    2.6 
             2  1.24428    1.7 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000001
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.23   |        0 ||
               1.5000  |   0.20   |        0  ||
               1.0000  |   0.18   |        0   |
[  1] 12:30:52   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:52   [NODE:2] Locus 9: Short chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     10.60529  
           Start-tree-ln(L)=ln P(D|G):                 -24.45267
           Pop. Theta    M
             1  1.14303 ------    2.2 
             2  0.98624    2.9 ------ 
 
           Maximization cycles needed: 13
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.27   |        0 ||
               1.5000  |   0.23   |        0  ||
               1.0000  |   0.26   |        0   |
[  2] 12:30:52   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:52   [NODE:1] Locus 10: Short chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.02145   
           Start-tree-ln(L)=ln P(D|G):                 -30.20108
           Pop. Theta    M
             1  1.24494 ------    2.7 
             2  1.56647    2.0 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.26   |        0 ||
               1.5000  |   0.21   |        0  ||
               1.0000  |   0.19   |        0   |
[  1] 12:30:52   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:52   [NODE:2] Locus 9: Short chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.58979   
           Start-tree-ln(L)=ln P(D|G):                 -32.14305
           Pop. Theta    M
             1  1.65228 ------    1.8 
             2  0.94718    2.5 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.27   |        0 ||
               1.5000  |   0.25   |        0  ||
               1.0000  |   0.24   |        0   |
[  2] 12:30:52   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:52   [NODE:1] Locus 10: Short chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.27266   
           Start-tree-ln(L)=ln P(D|G):                 -34.91104
           Pop. Theta    M
             1  1.65211 ------    2.9 
             2  2.05379    2.3 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000001
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.22   |        0 ||
               1.5000  |   0.19   |        0  ||
               1.0000  |   0.19   |        0   |
[  1] 12:30:52   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:53   [NODE:2] Locus 9: Short chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.44435   
           Start-tree-ln(L)=ln P(D|G):                 -31.37097
           Pop. Theta    M
             1  1.77406 ------    1.5 
             2  0.78003    4.1 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.28   |        0 ||
               1.5000  |   0.24   |        0  ||
               1.0000  |   0.20   |        0   |
[  2] 12:30:53   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:53   [NODE:1] Locus 10: Short chain   4:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.74747   
           Start-tree-ln(L)=ln P(D|G):                 -45.75113
           Pop. Theta    M
             1  1.89620 ------    3.4 
             2  2.15462    1.7 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.21   |        0 ||
               1.5000  |   0.21   |        0  ||
               1.0000  |   0.20   |        0   |
[  1] 12:30:53   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:53   [NODE:2] Locus 9: Short chain   4:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.64421   
           Start-tree-ln(L)=ln P(D|G):                 -41.13773
           Pop. Theta    M
             1  2.28935 ------    1.9 
             2  0.87241    5.4 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.25   |        0 ||
               1.5000  |   0.25   |        0  ||
               1.0000  |   0.21   |        0   |
[  2] 12:30:53   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:53   [NODE:1] Locus 10: Short chain   5:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     4.99422   
           Start-tree-ln(L)=ln P(D|G):                 -49.87402
           Pop. Theta    M
             1  2.78904 ------    3.1 
             2  2.81441    1.5 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000001
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.23   |        0 ||
               1.5000  |   0.18   |        0  ||
               1.0000  |   0.20   |        0   |
[  1] 12:30:53   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:53   [NODE:2] Locus 9: Short chain   5:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.57570   
           Start-tree-ln(L)=ln P(D|G):                 -27.82863
           Pop. Theta    M
             1  2.12309 ------    2.4 
             2  0.97948    7.9 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.26   |        0 ||
               1.5000  |   0.19   |        0  ||
               1.0000  |   0.23   |        0   |
[  2] 12:30:53   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:53   [NODE:1] Locus 10: Short chain   6:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.87693   
           Start-tree-ln(L)=ln P(D|G):                 -36.30024
           Pop. Theta    M
             1  2.82309 ------    2.5 
             2  3.06102    1.4 ------ 
 
           Maximization cycles needed: 9
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.24   |        0 ||
               1.5000  |   0.20   |        0  ||
               1.0000  |   0.19   |        0   |
[  1] 12:30:53   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:53   [NODE:2] Locus 9: Short chain   6:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.89859   
           Start-tree-ln(L)=ln P(D|G):                 -36.71118
           Pop. Theta    M
             1  2.97634 ------    2.8 
             2  1.08962    7.6 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.32   |        0 ||
               1.5000  |   0.22   |        0  ||
               1.0000  |   0.25   |        0   |
[  2] 12:30:53   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:54   [NODE:1] Locus 10: Short chain   7:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.51770   
           Start-tree-ln(L)=ln P(D|G):                 -49.23083
           Pop. Theta    M
             1  3.42463 ------    2.8 
             2  3.99139    1.6 ------ 
 
           Maximization cycles needed: 8
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.21   |        0 ||
               1.5000  |   0.21   |        0  ||
               1.0000  |   0.20   |        0   |
[  1] 12:30:54   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:54   [NODE:2] Locus 9: Short chain   7:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     4.25974   
           Start-tree-ln(L)=ln P(D|G):                 -29.82948
           Pop. Theta    M
             1  1.93107 ------    3.2 
             2  1.26868    6.7 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.31   |        0 ||
               1.5000  |   0.23   |        0  ||
               1.0000  |   0.26   |        0   |
[  2] 12:30:54   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:54   [NODE:1] Locus 10: Short chain   8:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.76687   
           Start-tree-ln(L)=ln P(D|G):                 -54.74770
           Pop. Theta    M
             1  3.98203 ------    3.1 
             2  3.78470    1.4 ------ 
 
           Maximization cycles needed: 8
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.22   |        0 ||
               1.5000  |   0.18   |        0  ||
               1.0000  |   0.20   |        0   |
[  1] 12:30:54   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:54   [NODE:2] Locus 9: Short chain   8:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.05217   
           Start-tree-ln(L)=ln P(D|G):                 -28.87114
           Pop. Theta    M
             1  2.10777 ------    2.7 
             2  1.40494    9.4 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.25   |        0 ||
               1.5000  |   0.24   |        0  ||
               1.0000  |   0.23   |        0   |
[  2] 12:30:54   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:55   [NODE:1] Locus 10: Short chain   9:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     6.61669   
           Start-tree-ln(L)=ln P(D|G):                 -44.19038
           Pop. Theta    M
             1  6.07967 ------    2.1 
             2  3.62767    1.5 ------ 
 
           Maximization cycles needed: 12
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.25   |        0 ||
               1.5000  |   0.19   |        0  ||
               1.0000  |   0.22   |        0   |
[  1] 12:30:55   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:55   [NODE:2] Locus 9: Short chain   9:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.36563   
           Start-tree-ln(L)=ln P(D|G):                 -26.98747
           Pop. Theta    M
             1  2.24936 ------    2.5 
             2  1.88784    8.8 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000001
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.28   |        0 ||
               1.5000  |   0.25   |        0  ||
               1.0000  |   0.23   |        0   |
[  2] 12:30:55   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:55   [NODE:1] Locus 10: Short chain  10:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     1.05990   
           Start-tree-ln(L)=ln P(D|G):                 -56.30244
           Pop. Theta    M
             1  5.59032 ------    1.7 
             2  3.81901    1.2 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000001
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.22   |        0 ||
               1.5000  |   0.18   |        0  ||
               1.0000  |   0.22   |        0   |
[  1] 12:30:55   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:55   [NODE:2] Locus 9: Short chain  10:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.53096   
           Start-tree-ln(L)=ln P(D|G):                 -36.67133
           Pop. Theta    M
             1  2.08441 ------    2.1 
             2  1.55422    7.3 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.27   |        0 ||
               1.5000  |   0.23   |        0  ||
               1.0000  |   0.23   |        0   |
[  2] 12:30:55   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:56   [NODE:1] Locus 10: Long chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     5.06087   
           Start-tree-ln(L)=ln P(D|G):                 -63.40395
           Pop. Theta    M
             1  7.50401 ------    1.6 
             2  4.72647    0.7 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.21   |        0 ||
               1.5000  |   0.21   |        0  ||
               1.0000  |   0.23   |        0   |
[  1] 12:30:56   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:56   [NODE:2] Locus 9: Long chain   1:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     0.74068   
           Start-tree-ln(L)=ln P(D|G):                 -33.91385
           Pop. Theta    M
             1  1.96835 ------    2.1 
             2  1.76591    6.2 ------ 
 
           Maximization cycles needed: 15
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.26   |        0 ||
               1.5000  |   0.24   |        0  ||
               1.0000  |   0.25   |        0   |
[  2] 12:30:56   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:56   [NODE:1] Locus 10: Long chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     3.86192   
           Start-tree-ln(L)=ln P(D|G):                 -79.36357
           Pop. Theta    M
             1  5.07128 ------    1.7 
             2  6.48024    0.7 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.25   |        0 ||
               1.5000  |   0.20   |        0  ||
               1.0000  |   0.26   |        0   |
[  1] 12:30:56   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:56   [NODE:2] Locus 9: Long chain   2:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     6.58501   
           Start-tree-ln(L)=ln P(D|G):                 -30.33813
           Pop. Theta    M
             1  2.04431 ------    3.9 
             2  2.11312    7.8 ------ 
 
           Maximization cycles needed: 10
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.26   |        0 ||
               1.5000  |   0.23   |        0  ||
               1.0000  |   0.25   |        0   |
[  2] 12:30:56   Burn-in (first 1000 trees are not used)
           Prognosed end of sampling is    12:31 May 12 2010
12:30:57   [NODE:1] Locus 10: Long chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     4.41453   
           Start-tree-ln(L)=ln P(D|G):                 -59.91776
           Pop. Theta    M
             1  6.66613 ------    2.1 
             2  5.86067    1.1 ------ 
 
           Maximization cycles needed: 11
           Norm of first derivatives:  0.000000
[  1] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.24   |        0 ||
               1.5000  |   0.20   |        0  ||
               1.0000  |   0.26   |        0   |
           Prognosed end of sampling is    12:31 May 12 2010
12:30:57   Multiple chain estimates:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     8.75113   
           Pop. Theta    M
             1  6.67905 ------    2.1 
             2  5.85595    1.1 ------ 
 
           Maximization cycles needed: 7
           Norm of first derivatives:  0.000000
           Prognosed end of sampling is    12:31 May 12 2010
12:30:57   [NODE:2] Locus 9: Long chain   3:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     2.66147   
           Start-tree-ln(L)=ln P(D|G):                 -37.66926
           Pop. Theta    M
             1  2.84088 ------    3.8 
             2  2.53341    6.9 ------ 
 
           Maximization cycles needed: 13
           Norm of first derivatives:  0.000000
[  2] Swapping between 4 temperatures.
           Temperature | Accepted |  Swaps between temperatures
                1e+06  |   1.00   |          |
               3.0000  |   0.31   |        0 ||
               1.5000  |   0.22   |        0  ||
               1.0000  |   0.26   |        0   |
           Prognosed end of sampling is    12:31 May 12 2010
12:30:57   Multiple chain estimates:
           ln L(Param)=ln (P(G|Param)/P(G|Param0)):     5.32295   
           Pop. Theta    M
             1  2.84088 ------    3.8 
             2  2.53341    6.9 ------ 
 
           Maximization cycles needed: 0
           Norm of first derivatives:  0.000000
12:30:57   Parameter estimation over all loci
           Printing likelihood ratio tests
-------------------------------------------------------------------------------
H0: 3.6195 2.5480 2.5480 3.6195                    | LnL(test) = -154.813626
 =  3.0600 3.0911 2.0050 4.1789                    | LnL(full) = -130.055736
[ m, m, m, m,]                                     | LRT       = 49.515781
                                                   | df        = 4
                                                   | Prob      = 0.000000
                                                   | Probc     = 0.000000
                                                   | AIC       = 313.627252
                                                   | num(param)= 2
-------------------------------------------------------------------------------
12:30:58   Calculating profile likelihoods for parameter  2 out of  4
12:30:58   Calculating profile likelihoods for parameter  1 out of  4
           Prognosed end of run: 12:30 May 12 2010
           Prognosed end of run: 12:31 May 12 2010
12:31:02   Calculating profile likelihoods for parameter  3 out of  4
12:31:02   Calculating profile likelihoods for parameter  4 out of  4
           Prognosed end of run: 12:30 May 12 2010
           Prognosed end of run: 12:30 May 12 2010
12:31:08   Program finished
