HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).

Biosequence analysis using profile hidden Markov models.

HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.

HUMAnN is a method for efficiently and accurately profiling the abundance of microbial metabolic pathways and other molecular functions from metagenomic or metatranscriptomic sequencing data.

Hypothesis Testing using Phylogenies. An open-source software package for comparative sequence analysis using stochastic evolutionary models.

inStrain is python program for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification.

InterProScan is the software package that allows sequences (protein and nucleic) to be scanned against InterPro's signatures. Signatures are predictive models, provided by several different databases, that make up the InterPro consortium.

ipyrad is an interactive assembly and analysis toolkit for restriction-site associated DNA (RAD-seq) and related data types.