This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.

The igvtools utility provides a set of tools for pre-processing data files.

A software package with various utilities for processing alignments in the SAM format, including variant calling and alignment viewing.

An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages.