Software for downloading
Inference from single-locus population-genetics data
genetree
This is software for the estimation of mutation, migration and growth rates, and ancestral inference such as the time to the most recent common ancestor of a sample of DNA sequences. It is available here.Gene tree with a single selected site: contact coop@stats.ox.ac.uk
Recombination estimation programs
Three program packages are available:- Paul Fearnhead (Fearnhead, P. and Donnelly, P. 2001. Estimating recombination rates from population genetic data. Genetics, 159:1299-1318)
- 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)
- Simon Myers (Myers, S. R. and Griffiths, R. C. 2003. Bounds on the minimum number of recombination events in a sample history. Genetics, 163:375-394).
Gil's program LDhat implements the approximate likelihood method of Hudson and is available here.
Simon's program RecMin is a program for directly detecting historical recombination events from sequence data, using a non-parametric approach. It is available here.
Which program to use?
For data without recombination, genetree is the natural choice. For particularly large problems, it might be prudent to compare results from genetree with Paul's programs with the recombination rate forced to be zero.For data sets where recombination cannot be ruled out, but where the user thinks they probably want to do a genetree-type analysis, we would suggest using one or both of the recombination programs in addition as a precaution.
Where recombination is an issue, it may also be interesting to use both Paul's and Gil's programs. The former should give better estimation, for data sets small enough for it to give reliable results, with the latter providing either a useful comparator in small problems, and the only currently available method from us when full likelihood isn't practicable.
popgen
popgen is an R package that specifically focuses on statistical and population genetics methods. The motivation behind the package is to produce an easy to use interface to many of the commonly used methods and models used in statistical and population genetics and an alternative interface for some of the methodology produced by our group.The package includes the following functionality
- Assess the level of population diversity between a set of populations using unlinked genotype data (popdiv).
- Estimate hidden population structure in unlinked genotype data using both parametric and non-parametric methods (ps, nps).
- Simulate haplotypes from a neutral coalecent process with recombination (treesim).
- Plot the linkage disequilibrium (LD) structure of a given set of haplotypes (LDmat).
- Simulate data from the Multinomial-Dirichlet model of population structure (simMD).
The package is available the following link popgen_0.0-2.tar.gz
A pre-compiled Windows binary is also available from the following link popgen_0.0-2.zip
Queries about the software should be addressed to Jonathan Marchini (marchini@stats.ox.ac.uk).
SelSim
When designing methods which provide the necessary power to detect regions of the genome which have experience historical selective pressures it is important to consider which patterns of genetic diversity are indicative of particular forms of natural selection. SelSim is a program which can simulate population genetic data in which a single site has experienced natural selection.
Go to SelSim command line program
Publication describing the package
Queries about the software should be addressed to Chris Spencer (spencer@well.ox.ac.uk).
Haplotype reconstruction
PHASE is a program for reconstructing haplotypes. The software is available for download from here.Queries about the software should be addressed to Matthew Stephens (stephens@stat.washington.edu).
Other software
structure and STRAT
Jonathan Pritchard's programs structure and STRAT have moved, with their author, to the University of Chicago. Click here to go to Jonathan's new home page[Home] [People] [Research] [Publications] [Software] [Events] [Jobs]
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