Phylogenetic Tree Methods

Phylogenetic tree construction is a major focus of our work, since phylogenomic analysis for protein function prediction assumes a (somewhat accurate) phylogenetic tree. Unfortunately, very little is known about which methods for phylogenetic tree construction really work on protein superfamilies.

We have a number of methods developed in our lab. These include Subfamily Classification in Phylogenomics (SCI-PHY), and Simultaneous Alignment and Tree Construction using Hidden Markov mOdels (SATCHMO).

Subfamily Classification In PHYlogenomics (SCI-PHY)

SCI-PHY is available online.

Papers on SCI-PHY:

• Sjölander, K, "Phylogenetic inference in protein superfamilies: Analysis of SH2 domains" Proceedings of the Conference Intelligent Systems for Molecular Biology 1998 6:165-74. PubMed abstract.

SATCHMO

SATCHMO is available online.

SATCHMO is also available for download from the Lobster website.

Papers on SATCHMO:

• Edgar, R., and Sjölander, K., "Simultaneous sequence alignment and tree construction using hidden Markov models." Proceedings of the Pacific Symposium on Biocomputing , HI. 2003; 180-91. PubMed Abstract.
• Edgar, R., and Sjölander, K., "SATCHMO: Sequence Alignment and Tree Construction using Hidden Markov models," Bioinformatics. 2003 Jul 22;19(11):1404-11. (Listed as a "must-read" by the Faculty of 1000.) Oxford University Press access.