Tabix

Generic indexer for TAB-delimited genome position files.

Kraken

Kraken is a taxonomic sequence classifier that assigns taxonomic labels to DNA sequences.

Dwgsim

Genome simulation 

Dfast

DFAST is a flexible and customizable pipeline for prokaryotic genome annotation as well as data submission to the INSDC

Cactus

Cactus is a reference-free whole-genome multiple alignment program

Alphafold

AI system that predicts a protein’s 3D structure from its amino acid sequence.

Lftp

LFTP is a sophisticated file transfer program supporting a number of network protocols (ftp, http, sftp, fish, torrent).

Pcrystal14

A program for the ab initio investigation of crystalline solids

Nbo

A discovery tool for chemical insights from complex wavefunctions. 

Gamess

The General Atomic and Molecular Electronic Structure System (GAMESS)
is a general ab initio quantum chemistry package.