Jody Hey                  Evolutionary Genetics

  Professor    -     Department of Genetics     -   Rutgers University

For Hey Lab Data Sets - Go HERE

Hey Lab Distributed Software

Software

I distribute several software programs for the analysis of DNA sequence based population genetic data. These programs have been developed over the years to suit my needs and those of people working in my lab.

All were written in C and the source code is available.  The programs should compile under different compilers.  A Win32 executable version (.exe file) is also available for each program.

The programs are a little bit interfunctional. SITES will generate input lines for the HKA and WH programs. The FPG program, in addition to its primary function, generates simulated data sets which can be read by SITES.

The programs can be freely distributed so long as no fee is charged for them.

• IM and IMa
• SIMDIV
• SITES 
• HKA 
• WH
• FPG

IM and IMa  - UPDATED 5/6/2009  (IMa had a bug dealing with loading Hapstrs with multiple STRs)

 

IM is a program, written with Rasmus Nielsen, for the fitting of an isolation model with migration to haplotype data drawn from two closely related species or populations.  IM is based on a method originally developed by Rasmus Nielsen and John Wakeley (Nielsen and Wakeley 2001 Genetics 158:885).  Large numbers of loci can be studied simultaneously, and different mutation models can be used. 

IMa implements the same Isolation with Migration model, but does so using a new method that provides estimates of the joint posterior probability density of the model parameters. IMa also allows log likelihood ratio tests of nested demographic models.  IMa is based on a method described in Hey and Nielsen (2007 PNAS 104:2785–2790).   IMa is faster and better than IM (i.e. by virtue of providing access to the joint posterior density function), and it can be used for most (but not all) of the situations and options that IM can be used for.

View the Inroduction to IM and IMa Documentation

View the Using IM Documention

View the Using IMa Documentation

Get the IM Distribution package - updated w/ significant bug fixes to IMa on 5/6/2009

Questions??  - try using the  Isolation with Migration Discussion Group .   This way common questions can be addressed by searching and discussion, and I can more easily manage my own communications about these topics.

Isolation with Migration

Visit this group

http://groups.google.com/group/Isolation-with-Migration

References:

Hey, J., and R. Nielsen. 2007. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. PNAS 104:2785–2790.

Hey, J. 2005. On the Number of New World Founders: A Population Genetic Portrait of the Peopling of the Americas. PLoS Biol 3:e193.

Won, Y. J., and J. Hey. 2005. Divergence population genetics of chimpanzees. Mol Biol Evol 22:297-307.

Hey, J., and R. Nielsen. 2004. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167:747-760.

Hey, J., Y.-J. Won, A. Sivasundar, R. Nielsen and J. A. Markert. 2004 Using nuclear haplotypes with microsatellites to study gene flow between recently separated populations. Molecular Ecology 13: 909-919

Nielsen, R., and J. Wakeley. 2001. Distinguishing migration from isolation. A Markov chain Monte Carlo approach. Genetics 158:885-96.

 

IM is subject to updates -- Click to email if you want to be notified of updates or news.

SIMDIV

SIMDIV is the program used in the Hey lab for generating data sets under an isolation with migration model. It can be used for multiple populations for a variety of mutation models – pretty much for any kind of data set for which IM and related programs can be used. SIMDIV is not the only program that can do this. There are lots of other coalescent simulators out there, and one that I know can be used for isolation with migration models is SIMCOAL, but there may be others. SIMDIV will simulate data with recombination if the users so specifies, even though IM programs assume no recombination. The program can handle up to 10 populations, with 350 gene copies per locus, for any number of loci. If desired a user can load all of the specifics associated with a real data set (# loci, sample sizes, mutation models, and IM parameter estimates) so that IM/SIMDIV results can be compared with the real data that was used to generate the parameter estimates. For IM users SIMDIV should be fairly easy to use because parameters mean the same things and are scaled the same way in SIMDIV and the IM programs.

View SIMDIV documentation

Download SIMDIV package

SITES

SITES is a computer program for the analysis of comparative DNA sequence data.  Basic analyses include: data summaries by polymorphism class;  polymorphism estimates within and between groups (species); estimates of migration, neutral model, and recombination parameters; and linkage disequilibrium analyses.  SITES is primarily intended for data sets with multiple closely related sequences. It is especially useful when multiple sequences have been obtained from each of one or several closely related populations or species.  

View SITES documentation

SITES Downloads

• WIN32 (Windows)  program

• WIN32 package (including documentation, sample data file,  and WIN32 program)

• Source code 

web page last updated June 16, 2009 .