An Alphabetic List
of
Genetic Analysis Software

PAGE 1 (A-F)

URL
master: http://www.nslij-genetics.org/soft/
mirror: http://linkage.rockefeller.edu/soft/
searchable database: http://www.animalgenome.org/soft/ (NEW!)

Last Update: March 16, 2012
Computer software on the following topics are 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 to that program from us.

In the last few years, new technology produces new types of genetic data, and the scope of genetic analyses change 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, yet be specialized topics by themselves. Though programs on variance calling from NSG can be in, those can sequence alignment might be out; programs on eQTL can be in, those on differential expression might be out.

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 takes its new home at North Shore LIJ Research Institute (2002-now). More than 240 programs have been listed by December 2004, more than 350 programs by August 2005, close to 400 programs by December 2006, close to 480 programs by November 2008, and 520 programs by August 2010. 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), and http://genamics.com/software/index.htm may contain archived copy of some programs.

More and more packages are now written in R. To be consistent, I rename any R package in CRAN from [package-name] to R/[package-name]. If a R package is not submitted to CRAN, I will keep its original name. Here is another partial list of statistical genetics R packages summarized by CRAN (http://cran.r-project.org/web/views/Genetics.html). Yet more R packages can be found in: 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/, among other places.

If you have new programs to add or any updated information, please send a message to webadm@nslij-genetics.org

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