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This page, historically known as 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, who then passed it on to his former student Gao Wang at the ASHG 2015 conference. 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 facilicate potential 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.
You can find github's search bar on the top of the page where you can search contents in this repository. Type in the keywords you care and see what you can find in this list! The formated pages are markdown files so you may want to restrict your search results to markdown format (you can customize your search filter after you run a search).
We welcome your input! Please follow the contribution guidelines to participate.
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 "Review" section for each program so that users can review the program and make recommendations to potential users. Link to "Review" sections are found at the end of program detail pages. Please also use this section to leave suggestions you have to pages on this list (please do not open any new issues for this).