Genetic Analysis Software

This page, historically known as the “Alphabetic List of Genetic Analysis Software”, or the “Rockefeller list”, is a list of computer programs for genetics analysis, including but not limiting to topics of:

• Genetic linkage analysis for human pedigree data
• QTL analysis for animal/plant breeding data
• Genetic marker ordering
• Genetic association analysis
• Haplotype construction
• Population genetics
• Genetic data visualization

This list is initially offered 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.

This list was created by Dr. Wentian Li when he was at Columbia University (1995-1996). It was later moved to Rockefeller University (1996-2002) and then to the North Shore LIJ Research Institute (2002-2013), maintained by Jurg Ott, which was then hosted on GitHub with help of his former student Gao Wang. 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. Since 2015, the list takes its home on github to allow for contributions from the community.

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.

Other genetic software lists can be found here.

We welcome your input! To contribute, please provide information of the software in markdown format by this template. You may include less sections than the template suggests (for example it may not have a version number or executable names), or more, as you see fit. Once you have completed the *.md file, you may either fork the repository, add the *.md file to content/genetic-analysis-software/pages folder, commit and send a github pull request; or you can simply email the *.md file to wang.gao@columbia.edu preferably with the phrase “Rockefeller List” in your email subject.

You are welcome to both add new software and make improvement to contents on existing software on the list.

Published software programs might have their user email-list or forum for technical discussions on usage and features of the software but they do not provide a general review that may be helpful to new customers who are shopping around trying to decide which product to go for. This list provides a “Discuss” (powered by disqus.com) section for each program so that users can review the program and make recommendations to potential users. For issues related to this site please open a github ticket.