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.
BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.
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.