PyCogent is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for: controlling third-party applications; devising workflows; querying databases; conducting novel probabilistic analyses of biological sequence evolution; and generating publication quality graphics.
IMPUTE2 is a computer program for phasing observed genotypes and imputing missing genotypes. Most people use just a couple of the program’s basic functions, but we have also built up a collection of specialized and powerful options. If you are new to IMPUTE2, or indeed to phasing and imputation in general, we suggest that you start by learning the basics.
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as against a single reference genome).
A software package that performs efficient inference of recombination in bacterial genomes. ClonalFrameML can be applied to any type of aligned sequence data, but is especially aimed at analysis of whole genome sequences.