index.md

The libsequence home page

This is the homepage for libsequence, which is a C++ library for evolutionary genetics.

Versions

The current "master" branch of the library is 1.8.3. This version represents a major change to the code base. The biggest change is that the library no longer requires boost or the GSL libraries. It still requires zlib. See the Revision History section in the README, which you can find at the GitHub repo for the project.

Source code

The library code is here

Library documentation

Reference manual

Programs using the library

There are lots of these:

• Thornton lab software page
• Kevin Thornton's GitHub account
• Thornton lab GitHub account

Some specific projects using the library

• pylibseq - A Python interface to libsequence.
• fwdpp - Forward simulation library described in Thornton (2014, doi: 10.1534/genetics.114.165019)
• pecnv - code from Rogers et al. (2014, doi: 10.1093/molbev/msu124) and Cridland et al (2013, doi: 10.1093/molbev/mst129) for detecting structural variants and transposable element insertions
• baldwin_brown_2014 - Code from Baldwin-Brown et al. (2014, doi: 10.1093/molbev/msu048) for simulating "evolve and resequence" experiments
• analysis
• sequtils
• msstats
• sweepsims - selective sweep code from Jensen et al. (2008, doi: 10.1371/journal.pgen.1000198), Thornton and Jensen 2007, doi: 10.1534/genetics.106.064642)
• newgene - copy-number variant simulation code from Thornton (2007, doi: 10.1534/genetics.107.074948)

Citation

If you use libsequence for yor research, or programs depending up on it, please cite the following paper:

• Thornton, K. (2003) libsequence, a C++ class library for evolutionary genetic analysis. Bioinformatics 19(17): 2325-2327 PMID 14630667 Manuscript, Software