Migrate 5.0.8

Released Summer 2025

Quick installation guide for the source code

from Github

Fastest way is the clone the gitub repository

  git clone https://github.com/pbeerli/migrate-5.0.7.git

in the top directory do: if you get the package from the github repository you will need
```
     autoreconf -i
```
If this fails: To install autoreconf, you need to install the Autotools build system. On Ubuntu use
```
    sudo apt-get install autoconf automake.
```
On macOS, you can use Homebrew with
```
    brew install autoconf automake
```
After installation, redo the
```
    autoreconf -i
```
Once that works use
```
    ./configure
```
or
```
    ./configure --enable-debug
```
and then do
```
    make
```
this should create the binary and if you have openmpi installed (check how to download for your system): it should also create the parallel version migrate-n-mpi. If this fails with errors (for example missing an include file)

try this:
```
    git submodule update --init --recursive
    cp ./lib/haru/win32/include/hpdf_config.h ./lib/haru/include/
    ./configure
    make
```
if this fails let me know.

If you want the binaries in an executable path you may want to do
```
    sudo make install
```
This will move the binaries to /usr/local/bin, if you do not have access to that use
```
./configure --prefix=/pathtoyourhomedirectory
make
make install
```
This will create a bin directory in your homedirectory, you still will need to check whether the bin directory is in the search PATH.

from my website

Download from my website: https://peterbeerli.com/migrate-html5/download_version4; Unpack the compressed distribution file. The binary distribution will have the executable migrate-n and migrate-n-mpi in the src, but little guarantee can be given that they work, I will need to write some detailed instructions for the parallel version because that will need additional software installed (openmpi). For UNIX and Mac use the source code distribution and compile for your machine, for windows, I will need to write compile instructions.

Content

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

Migrate estimates population parameters, effective population sizes migration rates and divergence times 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 Bayesian inference (BI). The output is presented in an TEXT file and in a PDF file. The PDF file contains all currently main tables, posterior histograms (BI) and skylineplots are supported in the PDF.

If you fail to see all plots in the outfile PDF, consider to use a non-adobe PDF reader. Recent Adobe Reader fails on some output files reporting empty histograms; other PDF-readers such as Preview.app on mac or Nitro PDF reader are fine.

Currently the following data types are supported: -DNA sequence data

finite sites model: Tamura-Nei and all models that can be expressed as a subset of Tamura-Nei
finite sites model + rate variation among sites: TN + Gamma

-SNP data (single nucleotide polymorphism)

SNP are derived from sampled sequences and are completely linked except that we know that the sites are variable, with resequencing project data I suggest NOT to use SNPS but the full sequences, the Bayes factor methods allows to break down into independent loci easily.

-Microsatellite data

Brownian motion model: a continuous approximation to the stepwise mutation model.
stepwise mutation model (if you want to finish your work in this century do not use this))

-Electrophoretic marker data (infinite allele model).

Analyses

[+ working and described

experimental and needs further description]

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 geographic effects can be removed out of the analysis, Estimation of mutation-scaled divergence time among populations.
Marginal likelihood calculation to assist calculation of Bayes Factor (BI)

Allows a variable mutation rate AMONG loci estimated from the data.
For sequences: allows a variable substitution rate among sites.

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.

Histogram of events over time
Plot of expected parameters through time (skyline plots) for all parameters.
Dated samples

Relabeling and merging of populations
Random subset of individuals per population

Assignment of indiviudals to populations (population number needs to be known)
Haplotype assignment (for small numbers of different haplotypes) and integration over all potential haplotype

Computer systems

You can fetch Migrate from the website http://popgen.sc.fsu.edu or http://peterbeerli.com/migrate-html5 as source code or binary executables. Currently I supply binaries for

Macintosh: migrate-n
Windows: migrate-n.exe

The source code should compile on all platforms (windows may be tricky) [see top]

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/ or https://peterbeerli.com/migrate-html5/index.html

Installation

(a) Binaries Unpack the compressed archive, open the directory migrate-5.x

Mac: from the binary distribution copy migrate-n to /usr/local/bin and then use the Terminal.app
Windows: the preferred way to use migrate-n.exe is through the commandline environment.
UNIX: I suggest to use the source distribution to make the best use of your system, then place the binary in /usr/local/bin or some other directory that is searched and then call migrate-n from the commandline.

Compiling the Source

Download the program 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 and MACs)

unpack the distribution file
cd migrate-VERSION/src
type “./configure” This will create the Makefile [./configure –help for more options]
type “make” (please report errors, there will be some warnings depending on your system).

The result of the compilation should be an executable “migrate-n” a parallel executable migrate-n-mpi in the src directory [it is called “migrate-n” because on some computer system there is a system program called “migrate”]
sudo make install This will install the programs and (outdated) man-page into usr/local/bin, /usr/local/man/man1 [you need to be root or administrator to do this; this step is NOT necessary, to use the program, but it would be convenient for all users of your system] if this does not work: move migrate-n to /usr/local/bin or $HOME/bin or some other convenient place.
change directory to “example” run “migrate-n parmfile.testbayes”, on my mac this takes a few minutes. If this test fails, 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. New versions of Acrobat have issues reading the PDF output file from migrate, if you see unfinished graphs in your output PDF use another viewer (for example NITRO PDF). On macs use Preview.app (it is anyway better than Acrobat Reader).

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-n parmfile.testbayes or the ml version.

Guidance

Look at the file GUIDANCE for some help when migrate is not delivering the answers you think it should deliver.

Fan-mail, complaints, questions and error-reports

Peter Beerli beerli@fsu.edu or migrate-support@googlegroups.com

Disclaimers

** MIT OPENSOURCE LICENSE*****************************************************************

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the “Software”), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
of the Software, and to permit persons to whom the Software is furnished to do
so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies
or substantial portions of the Software.
THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF
CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE
OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Last update: December 27 2025