The biological science divisions of the AMNH (Invertebrate Zoology, Vertebrate Zoology, and Paleontology) are involved in a broad variety of research projects concerning the evolutionary relationships of creatures of immense diversity, ranging from viruses, foraminifera, and sponges to arthropods, and vertebrates. The basic problem of reconstructing evolutionary trees falls into a class of problems known at NP-hard, i.e. non-deterministic polynomial-time hard. Researchers in these divisions are at the forefront of algorithmic innovation and implementation of combinatoric heuristics.
Researchers in the Invertebrate Zoology Division, lead by Chair Ward Wheeler have developled a series of heuristics to the tree-alignment problem and chromosomal alignment with moves. These ideas (and other existing approaches) have been implemented in our open source, freely available POY version 4 software (Varon et al., 2010; ), which was preceded by MALIGN.
The multiple alignment procedures implemented in MALIGN are close parallels to those used to search for minimum length cladograms. The logic and program commands will be clear to those familiar with programs such as Hennig86, NONA, and PAUP. Alignment topologies are constructed via different sequences and improved through branch swapping. Each alignment topology yields a multiple alignment and cladograms are constructed from that alignment. The cost of the most parsimonious cladogram is then assigned as the multiple alignment cost.
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.