-------------
Migrate 3.4.x
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3.4.4 released January  2013 

Quick installation guide 
------------------------
- Unpack the compressed distribution file
- Macos, Unix binary distributions: double click or commandline-execute the file: install_migrate
  [this will move the binary migrate-n and also migrateshell.app into place -- needs python]
- Source files: configure; make; sudo make install ;
  or other potential targets such as:  
  - on macs: make install_migrateshell
  - if you have openmpi installed: make mpis  

Content
-------
- Overview
- Analyses summary
- Computer systems
- History of MIGRATE
- Distribution
- Installation
- Documentation
- Example folder
- Troubleshoothing
- Disclaimer


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 (ML_ approach or Bayesian inference (BI).
The output is presented in an TEXT file and in a PDF file. The PDF file
eventually will contain all possible analyses including histograms 
of posterior distributions. Currently only main tables (ML + BI), 
profile likelihood tables (ML), percentiles tables (ML), and 
posterior histograms (BI) are supported in the PDF.
 
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.
-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. Allowing for a geographic distance matrix so that effects geographic
  can be removed out of the analysis.(ML + BI)
- Profile likelihood curves deliver approximate confidence intervals.(ML)
- Allows approximate likelihood ratio tests and model selection using
  Akaike's Information criterion. (ML)
- Marginal likelihood calculation to assist calculation of Bayes Factor (BI) [Improved]
- Plots of overall immigration and emigration per population. (ML)
- Allows a variable mutation rate AMONG loci. (ML [+BI])
- For sequences: allows a variable substitution rate among sites. (ML+BI)
- For microsatellites: allows the definition of repeatnumber and use of fragment length as input
- Facilitates analyses of multimodal search space distributions with heating
  scheme and/or multi-run analyses. (ML+BI)
- Histogram of migration events over time (ML + BI)
- Plot of expected parameters through time (skyline plots) for all sizes and migration rates. 
- Dated samples (ML + BI)
- Relabeling and merging of populations
- Random subset of individuals per population

Computer systems
----------------
You can fetch Migrate from the website http://popgen.sc.fsu.edu 
as source code or binary executables. Currently I supply binaries for

- Macintosh 
  - Macintosh Intel:    migrate-n
                        migrateshell.app (includes migrate-n and fastmigrate-n)
- Windows: migrate-n.exe 
           migrate-n-mpi.exe 
           (to run migrate-n-mpi.exe you will need to install openmpi [version 1.6])

The source code should compile on all platforms (windows may be tricky)

The file is compressed as tar.gz or as zip file. 	
The documentation contains information about
how to compile and use a parallelized version of migrate 
so that it can run concurrently on computer clusters
(using MPI [preferrably OpenMPI]).


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

Distribution
------------
Migrate can be fetched from the www-site 
http://popgen.sc.fsu.edu/ 


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-3.3.0.src.tar.gz | tar xf -
   or use 
   tar xvfz migrate-3.3.0.src.tar.gz
   [this creates a directory "migrate-3.3.0" with subdirectories 
   "src", and "examples" in it.]
2. cd migrate-3.3.0/src
3. type "./configure"
   This will create the Makefile [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 (non-Macintosh computer!) you perhaps want to try 
   "make thread" (this allows parallel execution of chains when 
   using the heating scheme). On Macs configure will use automatically the built in threading framework (GrandCentral)
   that will be faster than the standard threading. "make" will produce migrate with PDF support,
   this might not work on all machines, if it fails please tell me.

   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.

6. change directory to example
   run "migrate-n parmfile.testml" and "migrate-n parmfile.testbayes", 
   on my 2008 macosx laptop the Bayesian run using parmfile.testbayes took about 2 minutes.
   If these two tests fail, please let me know!

Documentation
-------------
You need to download it separately from
http://popgen.sc.fsu.edu/Downloads.html

It is a PDF file and called  migratedoc.pdf.
The pdf file can be viewed and printed using Acrobat 
or any other PDF viewer.


Examples
--------
In the directory "example" you can find some example data sets.
You might wan to try the two parmfiles.testml and parmfile.testbayes
Use the Terminal.app (on macosx), or xterm (Linux), or cmd (Windows),
change directory to the example directory and then execute
for mac and unix: ../migrate-n parmfile.testbayes
for windows: ..\migrate parmfile.testbayes
or the ml version.

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) 2004-2012, Peter Beerli, Tallahassee

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


Last update:
January 2 2013









