AWTY, BAMBE, BEAGLE, BEAST, BEAUti, Bio++, DataMonkey, DendroPy, DnaSP, ENCprime/SeqCount, FigTree, GARLI, genealogical sorting index (gsi), HyPhy, IMa2, jModelTest, JELLYFISH, LAMARC, MacClade, MEGA, Mesquite, MIGRATE-N, Modeltest, Mr- Bayes, PAML, PAUP*, PHYLIP, r8s, readseq, Seq-Gen, Sites, Structure, Structurama, Tracer, TreeStat, TreeView X

Publication
Concise Encyclopaedia of Bioinformatics and Computational Biology (pp. 33–34, 40, 45–46, 54, 135, 145, 156, 184–185, 219, 238, 271–272, 325, 330–331, 352–353, 372–373, 395, 407, 409, 428, 440, 460–461, 510–511, 516–517, 524–525, 607, 611, 672–663, 684, 701–702, 727, 741, 757). Wiley-Liss, 2nd edition