--------------
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 the www-site 
(http://evolution.gs.washington.edu/lamarc.html).
(http://www.csit.fsu.edu/~beerli/migrate.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-2.0.6.src.tar.gz | tar xf -
   or use 
   tar xvfz migrate-2.0.6.src.tar.gz
   [this creates a directory "migrate-2.0.6" 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 some machines, 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; or use the Intel compiler icc 
    on Linux machines] 	
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 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 computer 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 175 2005-12-02 14:51:23Z beerli $









