ABySS (Assembly By Short Sequences) is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.

AMOS is a collection of tools and class interfaces for the assembly of DNA reads.

antiSMASH is a gene cluster detector.

BamTools are a C++ API & command-line toolkit for working with BAM data.

BBmap is a program for Short read aligner for DNA and RNA-seq data.

Bcftools is a program for variant calling and manipulating VCFs and BCFs.

beagle-lib is a library of GPU based functions for phylogenetic analysis.

BEAST is a phylogenetic analysis program.