H I S T O R Y    O F      M I G R A T E 


[people] in brackets helped with resources or reported problems.
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                                     1999
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June 4         MIGRATE-N 0.7.1
               Division by 0 bug fixed in fst-calculation, this seems
               to bother only DEC Alphas.
June 1         MIGRATE-N 0.7
               Updated documentation, several minor things, warnings and error
               reporting should be more consistent, I am adding a section to
               the manual that describes all error/warning messages [partly
               done], the plotting graphics are more flexible now, but still
               need more work. You can specify the range and type of 
               axes (log-scale, std-scale), and if the migration parameter
               shall be plotted as M=m/mu or 4Nm. Fix of inconsistency 
               in migration value menu input [Reinaldo Brito]. 
               Fix of an error in the
               profile-method=FAST (it will need now more time to finish,
               because it is doing the final maximization over all other
               parameters), if you want its old behavior, that assumes that 
               Theta and M are not correlated [not a too bad assumption], 
               then use profile=YES:QUICK.  
March 8        MIGRATE-N 0.6.3
               Updated documentation (fixed errors in description of
               random-seed options, added important material 
               to profile-likelihood) , 
               inclusion of improved man page,
               fixed configure for SGI's with out gcc. 
Feb 14         MIGRATE-N 0.6.2 
               Tree traversal debug code removed,
               this killed runs with many individuals [Lisle Gibbs]
               Configure for SGI changed, does it work?
               MIGRATE-0.4: no change.
               Registered users: 280.
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                                     1998
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December 29    MIGRATE-N 0.6.1 Multilocus estimates are all wrong 
               in version 0.6, silly programming mistake found an fixed.
               If you have used microsatellites or electrophoretic markers
               or several sequence loci you need to rerun that analysis.
               Result table should print now nicer with population numbers 
               above 3.  
               MIGRATE-0.4: no change.
               Registered users: 234
Oct 29         MIGRATE-N 0.6
               Addition of datatype=n that is for single nucleotide
               polymorphism data, no simulation with this kind of data
               is yet done, so I do not know about biases etc. 
               Profile tables now report 4Nm instead of m/mu for
               the migration parameters.
               Documentation changed and contains now more about 
               how to read the outfile and what you can and 
               cannot do with the reported log(likelihood) values 
               [Mats Bjorklund].
               Binaries for OPENSTEP available [thanks to Magnus Nordborg
               giving me an account on his machine].
               Registered users: 206
Sep 1          MIGRATE-N 0.4/0.5 [was not released, was too busy with 
               other things]
               FST start values work now also for microsatellite data
               but I still need to check  the correctedness of the FST table
               when the data are microsatellites.
               Fixed wrong emmigration plots. Fixed wrong start 
               calculations for allelic data when a delimiter was used,
               and several minor bug fixes. Profile-method
               "uncorrelated" from version alpha.1 recovered.
               Registered users: 197
June 14        MIGRATE-N alpha.3 and MIGRATE-0.4.2
               Several minor changes in migrate-n: menu addition for
               -profile method: 
               profile-method=<Spline | Percentiles | Discrete>
               Spline: uses 1-dimensional splines to find percentiles,
               faster than the "Percentiles" option but not so accurate,
               "Discrete" evaluates at "fixed" (0.02, 0.1, 0.2, 0.5, 1, 2,
               5, 10, 50) * MLE of parameter.
               -with progress=yes you can see now a rough prognosed time 
               of end of sampling genealogies and if you use profiles 
               an estimated time of finishing.
               -Fix of reading in intermediate results (sumfile).
               -Most importantly a (hopefully) stable compile for 
               Windows, I failed to find the cause why the program
               compiled with WATCOM failed to finish with "bigger" data sets,
               it is now compiled with mingw32/gcc-win32, this is
               a windows port of the same system I am using on my workstation.
               Please report failures, I can only try a limited set of 
               examples.
               Migrate-0.4.2: new windows binary (using mingw32/gcc-win32)
               Registered users: 163
May 30         MIGRATE-N alpha.2 and MIGRATE-0.4.1
               With more than 2 sequence loci, there was a problem
               with the T/T-ratio, when the ratio was not specified 
               for each locus.
               Start parameter problems with microsatellite data fixed
               [Mats Bjorklund]. 
               Persistent problems with Windows executable
               sometimes I get floating point errors, on all other systems
               this does not occur.
               Registered users: 153
May 29         MIGRATE-N alpha.1 and MIGRATE-0.4
               Memory bug in FST calculation found and fixed
               [Daniel Yeh] 
               No change of Migrate-0.4
               Registered users: 148.
May 26         MIGRATE-N and MIGRATE-0.4
               This release has the two population version (Migrate-0.4) 
               and an alpha-version of Migrate-n that can solve migration
               matrix population model with unequal population sizes and
               unequal migration rates for n populations, I tried up to 10
               and the results where fine, but I am pretty sure that if 
               you try to feed in all your date of 100 subpopulation it
               will (a) probably crash, but more importantly (b) will
               need TERRIBLY long to run. 
               I would like to get some 
               feedback about what you want to see in the outfile,
               menu etc. Registered Users: ~138.
February 25    MIGRATE 0.4 (was not put up onto the website, I was to busy)
               More complex sequence evolution models (categories,
               weights, autocorrelation etc.) should work now, 
               it was broken. Cleanup of some output file lines, and
               some menu entries. The FST estimation (Remember FST is only 
               used to generate start parameter values) is 
               in pre 0.4 versions logically flawed. It estimates 
               2 parameters per population using F_within and F_between,
	       but there is only 1 F_between. Correctly, we can
               only estimate maximally 3 parameters with 1 locus for
               two populations. I added an option into the MENU and into
               the PARMFILE (fst-type=<Theta | Migration >) with which you 
               can decide which parameter is considered the same for both
               populations.
	       Registered users:89
------------------------------------------------------------------------
                                     1997
------------------------------------------------------------------------
August 20      MIGRATE 0.3.1
               Confusing menu entries for start theta and 4Nm values
               fixed [Carol Reeb], the start migration values are now
               4Nm and *not* m/mu values as before. Automatic Random
               number seed on Macs and perhaps on other Systems 
               delivered sometimes negative values, now fixed 
               [Carol Reeb], although I would recommend to use your
               own random number seeds: best values are 4n + 1 in the 
               range of 5 .. 2147483647, so there are plenty of 
               start random number seeds. Menu entry for
               usertree options should be no more clear, the usertree
               options needs a genealogy with migration events on
               it [Tony Metcalf]. Currently MIGRATE can construct 
               those, or you have to do it by hand, if you need to do 
               this send me email, because the doc is not updated. 
               Registered users:52
June 20        MIGRATE 0.3.0. 
               Brownian motion approximation to stepwise mutation
	       model for microsatellites added.  Solved problems:
	       Input problems with microsatellites data, major memory
	       allocation problem for datasets with more than 100
	       gene copies fixed [Carol Reeb].  Update of some
	       citation  and FST output tables [Byron Adams].
	       Persistent problems: Long sequences AND high number of
	       individuals need nuch longer chains than the proposed
	       default. Try ten times longer "long" chains. Or use
	       the option "moving-steps".  
               Registered users:38
May 12         MIGRATE 0.2.1a. 
               Fixed problems: Interleaved sequence data
	       should work now, last character of individual names is
	       now printing, and printing of second population data
	       should work, too, although the EP data printout is
	       still ugly.  [Allen Rodrigo]. Memory problem with some
	       Allelic data fixed.  
               Registered users: 30
April 30       MIGRATE 0.2a released.
	       Fixed problems or changes:  Corrections of several
	       minor problems, Printing of the data fixed, but still
	       ugly; Memory problem with large sequences fixed.
	       Options: treefile added, can write now a genealogy
	       with migrations; the option progress=Verbose for more
	       information during a run, the progress=Yes gives now
	       less information than before. Output: covariance
	       matrix for combined loci now prints, too.  Persistent
	       problems:  -Long sequences need very long chains to
	       remove the starting conditions for the migration rate
	       from the first tree (see documentation).
	       -Microsatellites still have probably a bias downwards
	       in Theta, but I need more simulations to make this
	       more clear.  
               Registered users: 8
March 4        First trial release of MIGRATE 0.1a
	       This release is not announced widely, because I have
	       to test, almost everything including all HTMLs,
	       registration, and the program itself: simulations need
	       time.  Registered users: 1







