BBmap is a program for Short read aligner for DNA and RNA-seq data.
BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence 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.
BEDTools are a set of utilities for genomics analysis.
Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.
BioBloom Tools (BBT) is a general use fast sequence categorization tool utilizing Bloom filters.