Bioinformatics Advance Access originally published online on October 27, 2004
Bioinformatics 2005 21(5):676-679; doi:10.1093/bioinformatics/bti079
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HyPhy: hypothesis testing using phylogenies
1 Antiviral Research Center, University of California San Diego San Diego, CA 92103, USA
2 Bioinformatics Research Center, North Carolina State University Raleigh NC 27695-7566, USA
*To whom correspondence should be addressed.
Summary: The HyPhypackage is designed to provide a flexible and unified platform for carrying out likelihood-based analyses on multiple alignments of molecular sequence data, with the emphasis on studies of rates and patterns of sequence evolution.
Availability: http://www.hyphy.org
Contact: muse{at}stat.ncsu.edu
Supplementary information: HyPhydocumentation and tutorials are available at http://www.hyphy.org
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Y.-L. Guo and S. Ge Molecular phylogeny of Oryzeae (Poaceae) based on DNA sequences from chloroplast, mitochondrial, and nuclear genomes Am. J. Botany, September 1, 2005; 92(9): 1548 - 1558. [Abstract] [Full Text] [PDF]
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C. T. T. Edwards, K. J. Pfafferott, P. J. R. Goulder, R. E. Phillips, and E. C. Holmes Intrapatient Escape in the A*0201-Restricted Epitope SLYNTVATL Drives Evolution of Human Immunodeficiency Virus Type 1 at the Population Level J. Virol., July 15, 2005; 79(14): 9363 - 9366. [Abstract] [Full Text] [PDF]
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S. L. Kosakovsky Pond and S. D. W. Frost Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection Mol. Biol. Evol., May 1, 2005; 22(5): 1208 - 1222. [Abstract] [Full Text] [PDF]
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