------------- Migrate 3.6.x ------------- 3.6 released Summer 2013 Quick installation guide ------------------------ - Unpack the compressed distribution file - Macos, Unix binary distributions: move the migrateshell.app to your /Applications folder - Source files: configure; make; sudo make install ; - 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) and skylineplots 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 - 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)) -Electrophoretic marker data (infinite allele model). Analyses -------- IMPORTANT: support will cease for approaches with *, approaches with ** are currently not supported (and often have an alternative) - 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.(BI + ML*) - 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) - 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 - Several prior settings for BI 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 the compressed archive, open the directory migrate-3.5.1 - Mac: in the Finder copy migrateshell.app to the /Applications folder (double clicking the migrateshell.app will open a terminal window set the internals so that you can run migrate-n and also fastmigrate-n [although this may not work on the first try because additional software needs to be installed (follow the online instructions). There is also a migrate-n binary in the folder that can be used, but it would be best if you plae that into a location like /usr/local/bin (and then adjust your search path to access it). - 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 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-3.5.1.src.tar.gz | tar xf - or use tar xvfz migrate-3.5.1.src.tar.gz [this creates a directory "migrate-3.5.1" with subdirectories "src", and "examples" in it.] 2. cd migrate-3.5.1/src 3. type "./configure" This will create the Makefile [./configure --help for more options] 4. There are several way to compile migrate. The most simple way us is just type "make" (please report warnings and especially errors). This will produce an executable for a single core computer. 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/make will use automatically the built in threading framework (GrandCentral) that will be faster than the standard threading. On multicore or cluste machine you may want to try in addition "make mpis" this creates a parallel version of migrate, more instructions under the parallel-readmes. "make" will produce migrate-n 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 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] 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! Troubleshooting --------------- - You cannot run configure or make: If you want to compile migrate yourself then you will need to install a developer framework on your computer, on Macs download Xcode and install the commandline tools. - You can run "configure" but the "make" command fails because it says something like "-lz not found or "gzgetc_" not found, then there are some issues with the compression library, because migrate fails to find all parts either from your system or the one supplied in the distribution. Do this: make clean cd zlib configure make cd .. make [this will help for most systems] 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-n parmfile.testbayes or the ml version. Fan-mail, complaints, questions and error-reports ------------------------------------------------- Peter Beerli beerli@fsu.edu or migrate-support@googlegroups.com Disclaimers ----------- Copyright 1997-2002 Peter Beerli and Joseph Felsenstein Copyright 2003-2008 Peter Beerli Copyright 2009-2015 Peter Beerli and Michal Palczewski 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: September 19 2013