HMMER: biological sequence analysis using profile HMMs

GUI/CommandLine Tool Box for biologistists to utilize NGS data.

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.

R/qtl: A QTL mapping environment

Genome Association Predict Integrate Tools

MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!

Graph-based alignment (Hierarchical Graph FM index)