DESeq is an R package to analyse count data from high-throughput sequencing assays such as RNA-Seq and test for differential expression. The latest version is DESeq2 (released April 2013).
A tool to visualise and analyse high throughput mapped sequence data
SeqMonk is a program to enable the visualisation and analysis of mapped sequence data
QuEST is a Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitations (ChIP-Seq or ChIPseq).
Various forms of alignment (including Smith-Waterman-Gotoh) of DNA/protein against a reference. Authors are Guy St C Slater and Ewan Birney from EMBL. C for POSIX.
A generic tool for pairwise sequence comparison
A generic tool for pairwise sequence comparison
The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated datasets. It supports a wide variety of data types and format, including short-read alignments in the SAM/BAM format. Data can be viewed from local files or ov...
BiQ Analyzer is a software tool for easy visualization and quality control of DNA methylation data. With more than 2,000 downloads so far, BiQ Analyzer has become a standard tool for processing DNA methylation data from bisulfite sequencing.