About COTseq

The COTseq has been developed in Dr. Mullins' Lab at the University of Washington as a web interface to estimate maximum likelihood phylogenetic tree from a set of aligned nucleotide or amino acid sequences, re-root the tree at the least squares point, Center Of Tree (COT), and reconstruct the COT sequence. It ueses PhyML package (version 3.0.1) to perform phylogenetic reconstruction under GTR (DNA) or LG (amino acid) evolutionary model, HyPhy package (version 2.0) to reconstruct COT tree and sequence. COT and its applications to HIV vaccine design are explained at length in the following references:

Nickle et al. 2003. Science. 7 March 2003. Vol. 299. no. 5612, pp. 1515-1518
Rolland et al. 2007. Journal of Virology. August 2007, Vol. 81, no. 16. pp. 8507-8514

Reference for PhyML:

Guindon, S. and Gascuel, O. (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol, 52, 696-704.

Reference for HyPhy:

Pond, S.L., Frost, S.D. and Muse, S.V. (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics (Oxford, England), 21, 676-679.

© 2009 Mullins Lab, University of Washington. All rights reserved.