
-------------
Migrate 0.7
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Released June 1 1999

Migrate estimates population parameters, 
effective population sizes and migration rates
of n populations, using genetic data.
It is a maximum likelihood estimator and uses a 
coalescent theory approach taking into account 
history of mutations and uncertainty of 
the genealogy. Currently the following data types
are supported:
-DNA sequence data (finite sites model: F84)
-SNP data (single nucleotide polymorphism)[But see HISTORY] 
-Microsatellite data (stepwise mutation model, brownian motion model)
-Electrophoretic marker data (infinite allele model).

History  and PERSISTENT PROBLEMS
--------------------------------
read the HISTORY file.

Distribution
------------
Migrate can be fetched from our www-site 
(http://evolution.genetics.washington.edu/lamarc.html).
Currently we have the following packages available:

Documentation:
migratdoc.pdf                 Documentation (PDF)
migratedoc.ps                 Documentation (Postscript)

Source:
migrate.tar.gz                Source
migrate.src.pm.sea.hqx        Source for powermac (Codewarrior Pro 4)

Binary: (you need to fetch the documentation, too!!)
migrate.alpha.tar.gz          Dec Alpha DUNIX binaries
migrate.linux.tar.gz          LINUX binaries
migrate.sunos.tar.gz          SunOS binaries
migrate.powermac.sea.hqx      Powermac binaries
migrate.win95.zip             WindowsNT/95 binaries


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

(a) Binaries
Unpack, donwload and read the documentation and enjoy. 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.tar.gz | tar xf -
   or use 
   tar xvfz migrate.tar.gz
   [this creates a directory "migrate" with subdirectories 
   "src", and "examples" in it.]
2. cd migrate/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.
4. type "make" (please report warnings and especially errors)
   the result should be an executable "migrate-n" in the src/migrate 
   directory and an other executable "migrate-0.4" in src/migrate-0.4.
   (migrate-n is the program for n populations, migrate-0.4 is the
    program for two population, described in the submitted paper)

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 and migrate-0.4 to $HOME/bin or some other convenient
   place.

(c) Source (Powermac)
1.  Unpack
2.  Open the migrate.mu file and make 
    (we compiled and tested with Metrowerks Professional 4). This creates the 
    program, for further information read the README in the Mac distribution.


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

It comes in two flavours: migdoc.ps and migdoc.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 poscript
file and do:
on UNIX systems:  lpr migdoc.ps
on Macs:  by using the Laserwriter Utility program, and then by dowloading 
migdoc.ps to the printer, or dragging the the migdoc.ps file onto
the default-printer icon.
on Windows95/NT: copy migdoc.ps lpt1:
 
Example
-------
In the directory "example" is a full run of some arbitrary sequence data,
with infile, outfile, mathfile, and log.
In addition I added a small Mathematica package (lamarc.m) and an example
Mathematica notebook. 
It shows how you can create pretty plots of the mathfile,
which is the data used in the contour plots in the outfile.

Disclaimer
----------
This software is distributed free of charge 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) 1997-1999, Peter Beerli and Joseph Felsenstein, Seattle.

Fan-mail, complaints, questions and error-reports
-------------------------------------------------
Peter Beerli
beerli@genetics.washington.edu


Last update:
June 1, 1999




