An Alphabetic List
of
Genetic Analysis Software

Last updated: 10 November 2013

Computer software on the following topics is included here: genetic linkage analysis for human pedigree data, QTL analysis for animal/plant breeding data, genetic marker ordering, genetic association analysis, haplotype construction, pedigree drawing, and population genetics. This list is offered here as a service to the gene mapping community. The inclusion of a program should not be interpreted as an endorsement from us.

In the last few years, new technology has been producing new types of genetic data, and the scope of genetic analyses changes dramatically. It is no longer obvious whether a program should be included or excluded from this list. Topics such as next-generation-sequencing (NGS), gene expression, genomics annotation, etc. can all be relevant to a genetic study, but we'll have to decide on a case-by-case basis whether to include a program (email us if you are interested in having a program listed here).

This page was created by Dr. Wentian Li, when he was at Columbia University (1995-1996). It was later moved to Rockefeller University (1996-2002) and now it takes its home at North Shore LIJ Research Institute (2002-now). The present copy is maintained by Jurg Ott as a single file. More than 240 programs were listed by December 2004, close to 400 programs by December 2006, close to 480 programs by November 2008, and over 600 programs by October 2012. A version of the searchable database was developed by Zhiliang Hu of Iowa State University, and a recent round of updating was assisted by Wei JIANG of Harbin Medical School.

Some earlier software can be downloaded from EBI: ftp://ftp.ebi.ac.uk/pub/software/linkage_and_mapping/ (Linkage and Mapping Software Repository).

More and more packages are now written in R. To be consistent, any R package in CRAN has been renamed from [package-name] to R/[package-name]. If an R package is not submitted to CRAN, its original name has been kept. Here is another partial list of statistical genetics R packages summarized by CRAN: http://cran.r-project.org/web/views/Genetics.html. More R packages yet can be found at: http://www.mrc-epid.cam.ac.uk/~jinghua.zhao/r-genetics.htm, http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm, http://wpicr.wpic.pitt.edu/WPICCompGen/software.htm, http://www-gene.cimr.cam.ac.uk/clayton/software/, and other places.