Phylogenetic Analysis of DNA and other data using dynamic homology
POY is a phylogenetic analysis program that supports multiple kinds of data (e.g. morphology, nucleotides, genes and gene regions, chromosomes, whole genomes, etc). POY is particular in that it can perform true alignment and phylogeny inference (i.e. input sequences need not to be prealigned). Insertions, deletions, and rearrangements, can then be included in the overall tree score (under Maximum Parsimony), or in the model (under Maximum Likelihood). A variety of heuristic algorithms have been developed for this purpose and are implemented in POY.
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The development of POY4 is sponsored in part by CIPRES.
Varón, A., L. S. Vinh, W. C. Wheeler. 2010. POY version 4: phylogenetic analysis using dynamic homologies. Cladistics, 26:72-85.
Varón, A., L. S. Vinh, W. C. Wheeler. 2010. POY version 4: phylogenetic analysis using dynamic homologies. Cladistics, 26:72-85.
Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.1.1. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.1. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0.2911. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0.2885. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0.2870. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0 Beta 2635. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0 Beta 2602. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0 Beta 2398. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0 Beta 2318. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0 Beta 2205. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0 Beta 1983. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0 Beta 1908. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0 Beta 1902. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0 Beta 1724. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
Varón, A., L. S. Vinh, I. Bomash, W. C. Wheeler. 2008. POY 4.0 Beta 1665. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
Converts POY output (one or more trees in nested parentheses format) into a matrix (in hennig format) of group inclusion characters representing the concensus tree used for contraint files.
Datasets for published studies are available here for download. Descriptions of datasets and formats for each study are provided in the associated readme files.
Arango, C. P., and W. C. Wheeler. 2007. Phylogeny of the sea spiders (Arthropoda, Pycnogonida) based on direct optimization of six loci and morphology. Cladistics 23:00-00: 0-00.
Grant, T., D. R. Frost, J. P. Caldwell, R. Gagliardo, C. F. B. Haddad, P. J. R. Kok, B. D. Means, B. P. Noonan, W. Schargel and W. C. Wheeler. 2006. Phylogenetic systematics of dart-poison frogs and their relatives (Anura: Athesphatanura: Dendrobatidae). Bulletin of the American Museum of Natural History 299: 1-262.
Frost, D.R., T. Grant, J. Faivovich, R. Bain, A. Haas, C.F.B. Haddad, R.O. de Sá, S.C. Donnellan, C.J. Raxworthy, M. Wilkinson, A. Channing, J.A. Campbell, B.L. Blotto, P. Moler, R.C. Drewes, R.A. Nussbaum, J.D. Lynch, D. Green, and W.C. Wheeler. 2006. The amphibian tree of life. Bulletin of the American Museum of Natural History 297: 1-370.