--------------
Migrate 2.0.6
--------------
Released May 2005

Migrate estimates population parameters, effective population sizes
and migration rates of n populations, using genetic data.  It 
uses a coalescent theory approach
taking into account history of mutations and uncertainty of the
genealogy. The estimates of the parameter values are achieved by
either a Maximum likelihood approach or by a Bayesian approach.
 
Currently the following data types are supported:

-DNA sequence data
 - finite sites model: F84, Kimura two-parameter
 - finite sites model + rate variation among sites: 
   F84 + Gamma, F84 + arbitrary rates
-SNP data (single nucleotide polymorphism)
 - SNP are derived from sampled sequences and are completely linked
   except that we know that the sites are variable [not thoroughly tested] 
-Microsatellite data 
 - stepwise mutation model
 - brownian motion model: a continuous approximation to the stepwise mutation model.
   the approximation breaks down when the population sizes are small (Theta<5)
-Electrophoretic marker data (infinite allele model).

Analyses
--------
- Estimation of population sizes and migration rates of a migration matrix
  model, or arbitrarily subsets of a migration matrix model, or an n-island
  model.
- Profile likelihood curves deliver approximate confidence intervals.
- Allows approximate likelihood ratio tests and model selection using 
  Akaike's Information criterion. 
- Plots of overall immigration and emigration per population.
- Allows a variable mutation rate AMONG loci.
- For sequences: allows a variable substitution rate among sites.
- Facilitates analyses of multimodal search space distributions with heating
  scheme and/or multi-run analyses.

Computer systems
----------------
You can fetch Migrate from the website http://evolution.gs.washington.edu/lamarc/migrate.html or from http://www.csit.fsu.edu/~beerli/migrate.html 
as source code (tar.gz compressed) or as comiled binaries for Macos X, Linux on Intel,
Sun Solaris, and Windows. The documentation contains information about
how to compile and use a parallelized version of migrate 
so that it can run concurrently on computer clusters.


History about bug fixes and new features
----------------------------------------
read the HISTORY file.

Distribution
------------
Migrate can be fetched from our www-site 
(http://evolution.gs.washington.edu/lamarc.html).


Installation
------------

(a) Binaries
Unpack, download and read the documentation and try the program
on a small data set.
 
For UNIX systems
the binary can go to standard directories (e.g. /usr/local/bin),
the rudimentary man page can go to the /usr/local/man/man1.

(b) Source (UNIX)
1. gunzip -c migrate-2.0.3.src.tar.gz | tar xf -
   or use 
   tar xvfz migrate-2.0.3.src.tar.gz
   [this creates a directory "migrate-2.0.3" with subdirectories 
   "src", and "examples" in it.]
2. cd migrate-2.0.3/src
3. type "./configure"
   This will create the Makefile, I am not yet very skilled in 
   writing configuration files, but your feedback will help to 
   improve this.
   [on COMPAQ/DEC Alpha with with the TRU64 cc compiler, you can 
    squeeze out a little more speed by trying to use
    if you use the bash shell: CC=cc ./configure or if you use
    a csh shell type: env CC=cc ./configure] 	
4. type "make" (please report warnings and especially errors).
   If you have a multiprocessor machine you perhaps want to try 
   "make thread" (this allows parallel execution of chains when 
   using the the heating scheme).
   The result of the compilation should be an executable 
   "migrate-n" in the src directory [it is called "migrate-n" because
   on some system there is a system program called "migrate"]

5. make install 
   This will install the programs and man-page into usr/local/bin, 
   /usr/local/man/man1
   [you need to be root to do this; this step is not necessary, 
   to use the program, but it would be convenient for all users
   of your system]
   or 
   move migrate-n to $HOME/bin or some 
   other convenient place.



Documentation
-------------
You need to download it separately from
ftp://evolution.gs.washington.edu/lamarc/migrate
or through 
http://evolution.gs.washington.edu/lamarc/migrate.download.html

It comes in two flavors: migratedoc.ps and migratedoc.pdf.
The pdf file can be viewed and printed using Acrobat 
or another PDF viewer.  The ps file can be viewed using ghostscript.
If you have a printer capable of using postscript you can use 
the postcript file and do: 
-on UNIX systems:  lpr migratedoc.ps
-on Macs:  drag the file onto the desktop printer icon or 
 by using the Laserwriter Utility program, and then by gloating 
 migdoc.ps to the printer.
-on Windows95/NT: copy migratedoc.ps lpt1:
 
Examples
--------
In the directory "example" you can find some example data sets.

Disclaimers
-----------
This software is distributed free of charge for non-commercial use
and is copyrighted. Of course, we do not guarantee that the software 
works and are not responsible for any damage you may cause or have.

Copyright
---------
(c) 1997-2003, Peter Beerli and Joseph Felsenstein, Seattle.
(c) 2004, Peter Beerli, Tallahassee

Fan-mail, complaints, questions and error-reports
-------------------------------------------------
Peter Beerli
beerli@csit.fsu.edu


Last update:
$Id: README,v 1.39 2004/12/15 22:05:20 beerli Exp $









