--------------
Migrate 1.2 
--------------
Released July 2001

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, 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
 - SNP were derived in a panel-population of which we have no data
   except that we know that the sites are variable [not thorrowly tested] 
-Microsatellite data 
 - stepwise mutation model
 - brownian motion model: a continous approximation to the stepwise mutation model.
   the approximation breakes 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 approximative confidence intervals.
- Plots of overall immigration and emmigration per population.
- Allows a variable mutation arate AMONG loci.
- For sequences: allows a variable substition rate among sites.
- Facilitates analyses of multimodal search space distributions with heating
  scheme and/or multi-run analyses.

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 migrate packages available:

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

Source only:
migrate-1.1.src.tar.gz          Source (UNIX style)

Binary + Source: (you need to fetch the documentation, too!!)
[some of these are not yet ready]
migrate-1.1.macosx.tar.gz       MacOS X binary
migrate-1.1.LinuxPPC.tar.gz     Powermac LINUX binary
migrate-1.1.LinuxIntel.tar.gz   Intel LINUX binary
migrate-1.1.alpha.tar.gz        Dec Alpha DUNIX binary
migrate-1.1.sunos.tar.gz        SunOS binaries
migrate-1.1.sea.hqx             Macintosh Powermac binary
migrate-1.1.windows.zip         WindowsNT/95/98/2000 binary


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

(a) Binaries
Unpack, donwload 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-1.1.src.tar.gz | tar xf -
   or use 
   tar xvfz migrate-1.1.src.tar.gz
   [this creates a directory "migrate-1.1" with subdirectories 
   "src", and "examples" in it.]
2. cd migrate-0.9/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 
   [migrate-n is the program for n populations 
   (Beerli & Felsenstein, submitted). I unbundled the older version,
   migrate-0.4, it was described in Beerli & Felsenstein 1999, Genetics.
   If you still need that goto to the "oldstuff" directory on
   http:evolution.genetics.washington.edu/lamarc/migrate.download.html.]

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.

(c) Source (Powermac)
1.  Unpack
2.  Open the migrate-1.1.mcp file and make 
    (we compiled and tested with Metrowerks Professional 6). 
    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-0.9.ps and migdoc-0.9.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-0.9.ps
-on Macs:  drag the file onto the desktop printer icon or 
 by using the Laserwriter Utility program, and then by dowloading 
 migdoc-0.9.ps to the printer.
-on Windows95/NT: copy migdoc-0.9.ps lpt1:
 
Example
-------
In the directory "example" is a full run of some arbitrary sequence 
data, with infile, outfile, mathfile, and log.


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) 1997-2000, Peter Beerli and Joseph Felsenstein, Seattle.

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


Last update:
$Id: README,v 1.22 2001/05/23 06:00:16 beerli Exp $






