Fasta2 (pairwise local alignment program)

MUSCLE (protein multiple sequence alignment software)

NJplot (tree drawing)

NorMD (scoring function for multiple sequence alignments)

PDB (3D biological macromolecular structure data)

PHYML (maximum likelihood-based phylogeny inference)

ProFit (GNU program for protein least-squares fitting)

PyMOL (GNU software for molecular visualization)