Software that allows to infer population genetic parameters and use the coalescent

[coalesce logo] [fluctuate logo] [migrate logo] [recombine logo] [LAMARC logo] [micsat logo]

Lamarc programs: httpd://evolution.gs.washington.edu/lamarc.html

Maintainer: Mary K. Kuhner, Peter Beerli, Jon Yamato, and Joe Felsenstein, University of Washington, Seattle WA
[Coalesce icon] Coalesce estimates the effective population size of a single constant population using nonrecombining sequences.
[Fluctuate icon] Fluctuate estimates the effective population size and a exponential growth rate of a single growing population using nonrecombining sequences.
[Migrate icon] Migrate estimates the effective population sizes and migration rates of n constant populations using nonrecombining sequences, microsatellite data or enzyme electrophoretic data. It can run multiple loci in parallel on computer clusters.
[Recombine icon] Recombine estimates the effective population size and per-site recombination rate of a single constant-size population.
[Lamarc icon] Lamarc estimates the effective population sizes and migration rates, per-site recombination rate of n constant or exponentially growing/shrinking populations using sequence data or microsatellite data.

Rasmus Nielsen's programs:
http://www.biom.cornell.edu/Homepages/Rasmus_Nielsen/files.html

MDIV MDIV is a program that will simultaneously estimate divergence times and migration rates between two populations under the infinite sites model and under a finite sites model (HKY). The program can be used to test if there is evidence for migration between two populations or evidence for shared recent common ancestry. In addition, you get maximum likelihood estimates of the demographic parameters. The program assumes that there is no recombination. The output of the program are integrated likelihood surfaces for the three parameters: Theta (two times the effective population size times the mutation rate), M (2 times the migration rate) and T (the divergence time divided by the effective population size. For more information regarding the program, please see Nielsen, R. and J. W. Wakeley. 2001. Distinguishing Migration from Isolation: an MCMC Approach. Genetics 158: 885-896
Windows binary only, for source code send enquiries to the author.
MISAT MISAT is a program for estimating the likelihood surface for ? (4 times the effective population size times the mutation rate) for microsatellite data. Two models are implemented: a stepwise mutation model and a mutation model allowing multi-step mutations, i.e. mutational jumps larger than on repeat unit in size. There are several other programs available for doing this type of analysis, and to my knowledge, this is probably the slowest program publicly distributed. It is, by now, somewhat outdated although the multi-step mutational model probably is not implemented in any other programs. For more information, please see Nielsen, R. 1997. A Maximum Likelihood Approach to Population Samples of Microsatellite alleles. Genetics. 146: 711-716, Nielsen R. 1997. A likelihood approach to populations samples of microsatellite alleles (vol 146, pg 711, 1997). Genetics 147: 349-349, and Nielsen, R. and P. J. Palsboll. 1999. Tests of Microsatellite Evolution: Multi-Step Mutations and Constraints on Allele Size. Mol. Phyl. Evol. 11: 477-484.
Windows binary only, for source code send enquiries to the author.

Oxford group and associates:
http://www.stats.ox.ac.uk/mathgen/software.html

genetree A unique gene tree describing the mutation history of a sample of DNA sequences can be can be constructed as a perfect phylogeny under an assumption of non-recurrent point mutations. Genetree constructs such trees from DNA data and computes maximum likelihood estimates of mutation, migration and growth rates in the population. It also computes the distribution of the time to the most recent common ancestor and ages of mutations in gene trees. Geographical information as to which subpopulation mutations occurred in and where the most recent common ancestor of the sequences was is also computed. A companion program treepic has flexible output for producing postscript gene tree pictures. Version 9.0 is much faster in generating times in subdivided and exponentially growing populations than Version 8.3.
Source code is available and a compiled version for PC use are included in the zip file. The source code is portable and compiles under gcc.
Recombination Two program packages are available: one from Paul Fearnhead (Fearnhead, P. and Donnelly, P. 2001. Estimating recombination rates from population genetic data. Genetics, 159:1299-1318) and one from Gil McVean (McVean, G., Awadalla, P. and Fearnhead, P. 2002. A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics, 160:1231-1241).
infs, fins Paul's programs estimate the full-likelihood surface for the scaled mutation and recombination parameters from population-genetics data.
LDhat Gil's program LDhat implements the approximate likelihood method of Hudson.

Ian Wilson's group:
http://www.maths.abdn.ac.uk/~ijw/downloads/download.htm

[micsat icon] MICSAT: a program to calculate the effective population size from microsatellite data.
Batwing BATWING: a program to calculate the effective population sizes and growth rates from microsatellite data, assuming there was a split into several populations in the past.

Marc Beaumont's group:
http://www.rubic.rdg.ac.uk/~mab/software.html

Counter was started on March 4th 2002.

Page maintained by
Peter Beerli (beerli@csit.fsu.edu), CSIT and Biological Sciences, Florida State University, Tallahassee FL 32306-4120, USA
[This page is incomplete, but I intend to update it regularly, if you know programs that are missing fron the list, let me know and I might add them.]