POY version 5: Phylogenetic analysis using dynamic homologies under multiple optimality criteria

Cladistics

Volumn 31, Issue 2, 2015, Pages 189-196

  Wheeler, Ward C ^a   Lucaroni, Nicholas ^a   Hong, Lin ^a   Crowley, Louise M ^a   Varón, Andrés ^a  

^a DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84923342140     PISSN: 07483007     EISSN: 10960031     Source Type: Journal    
DOI: 10.1111/cla.12083     Document Type: Article

References (47)

1. Akaike, H., 1974. A new look at the statistical model identification. IEEE Trans. Automat. Contr. 19, 716-723.
2. Arango, C.A., Wheeler, W.C., 2007. Phylogeny of the sea spiders (Arthropoda, Pycnogonida) based on direct optimization of six loci and morphology. Cladistics 23, 255-293.
3. Barry, D., Hartigan, J., 1987. Statistical analysis of hominid molecular evolution. Stat. Sci. 2, 191-210.
4. Danelluto, M.R., DiCosimo, A., 2012. A "minimal disruption" skeleton experiment: seamless map & reduce embedding in ocaml. Procedia Comput. Sci. 9, 1837-1846.
5. Darling, A.C., Mau, B., Blattner, F.R., Perna, N.T., 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14, 1394-1403.
6. Denton, J., Wheeler, W.C., 2012. Trivial alignments in maximum likelihood analysis of nucleotide data. Cladistics 28, 514-528.
7. Farris, J.S., 1972. Estimating phylogenetic trees from distance matrices. Am. Nat. 106, 645-668.
8. Felsenstein, J., 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368-376.
9. Felsenstein, J., 1984. Distance methods for inferring phylogenies: a justification. Evolution 38, 16-24.
10. Giribet, G., Edgecombe, G.D., 2013. Stable phylogenetic patterns in scutigeromorph centipedes (myriapoda: Chilopoda: Scutigeromorpha): dating the diversification of an ancient lineage of terrestrial arthropods. Invertebr. Syst. 27, 485-501.
11. Giribet, G., Wheeler, W.C., 1999. The position of arthropods in the animal kingdom: Ecdysozoa, islands, trees and the 'parsimony ratchet'. Mol. Phylogenet. Evol. 10, 1-5.
12. Giribet, G., Wheeler, W.C., 2001. Some unusual small-subunit ribosomal DNA sequences of metazoans. Am. Mus. Novit. 3337, 1-14.
13. Gladstein, D.S., Wheeler, W.C. 1997. POY version 2.0. program and documentation available at http://research.amnh.org/scicomp/projects/poy.php. American Museum of Natural History, New York.
14. Goloboff, P.A. 1999. NONA (No Name) ver. 2. Published by the author. Tucumán, Argentina.
15. Goloboff, P., Farris, S., Nixon, K., 2003. TNT (Tree analysis using New Technology) version 1.0 ver. beta test v. 0.2. program and documentation available at http://www.lillo.org.arg/phylogeny/tnt. Published by the authors. Tucumán, Argentina.
16. Hasegawa, M., Kashino, H., Yano, T., 1985. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22, 160-174.
17. Janies, D., Hill, A.W., Guralnick, R., Habib, F., Waltari, E., Wheeler, W.C., 2007. Genomic analysis and geographic visualization of the spread of avian influenza (H5N1). Syst. Biol. 56, 321-329.
18. Jukes, T.H., Cantor, C.R., 1969. Evolution of protein molecules, pp. 21-132. In Munro, N.H. (ed.), Mammalian Protein Metabolism. Academic Press, New York.
19. Kimura, M., 1980. A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111-120.
20. Kluge, A.G., 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38, 7-25.
21. Moilanen, A., 1999. Searching for most parsimonious trees with simulated evolutionary optimization. Cladistics 15, 39-50.
22. Neyman, J. 1971. Molecular studies in evolution: a source of novel statistical problems. In Gupta, S.S., Yackel, J. (eds.), Statistical Decision Theory and Related Topics, pp. 1-27. Academic Press, New York.
23. Rannala, B., Yang, Z., 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43, 304-311.
24. Robinson, D.F., Foulds, L.R., 1981. Comparison of phylogenetic trees. Math. Biosci. 53, 131-147.
25. Schulmeister, S., Wheeler, W.C., 2004. Comparative and phylogenetic analysis of developmental sequences. Evol. Dev. 6, 50-57.
26. Schwarz, G., 1978. Estimating the dimension of a model. Ann. Stat. 19, 205-221.
27. Stamatakis, A., Ludwig, T., Meier, H., 2005. Raxml-iii: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21, 456-463.
28. Steel, M., Penny, D., 2000. Parsimony, likelihood, and the role of models in molecular phylogenetics. Mol. Biol. Evol. 17, 839-850.
29. Sugiura, N., 1978. Further analysis of the data by Akaike's information criterion and the finite corrections. Commun. Stat. Theory Methods 7, 13-27.
30. Tamura, H., Nei, M., 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10, 512-526.
31. Tavaré, S., 1986. Some probabilistic and statistical problems on the analysis of DNA sequences. Lect. Math. Life Sci. 17, 57-86.
32. Thorne, J.L., Kishino, H., Felsenstein, J., 1991. An evolutionary model for maximum likelihood alignment of DNA sequences. J. Mol. Evol. 33, 114-124.
33. Tuffley, C., Steel, M., 1997. Links between maximum likelihood and maximum parsimony under a simple model of site substitution. Bull. Math. Biol. 59, 581-607.
34. Varón, A., Wheeler, W.C., 2012. The tree-alignment problem. BMC Bioinformatics 13, 293.
35. Varón, A., Vinh, L. S., Bomash, I., Wheeler, W.C. 2008. Poy 4.0. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php.
36. Varón, A., Vinh, L.S., Wheeler, W.C., 2010. POY version 4: phylogenetic analysis using dynamic homologies. Cladistics 26, 72-85.
37. Vinh, L., Varón, A., Wheeler, W.C., 2006. Pairwise alignment with rearrangement. Genome Inform. 17, 141-151.
38. Vinh, L., Janies, A.V.D., Wheeler, W.C., 2007. Towards phylogenomic reconstruction. In Proceedings of the 2007 International Conference on Bioinformatics and Computational Biology, pp. 98-104, Las Vegas, NV, USA.
39. Wheeler, W.C., 1996. Optimization alignment: the end of multiple sequence alignment in phylogenetics? Cladistics 12, 1-9.
40. Wheeler, W.C., 1999. Fixed character states and the optimization of molecular sequence data. Cladistics 15, 379-385.
41. Wheeler, W.C., 2006. Dynamic homology and the likelihood criterion. Cladistics 22, 157-170.
42. Wheeler, W.C., 2007. Chromosomal character optimization. Mol. Phylogenet. Evol. 44, 1130-1140.
43. Wheeler, W.C., 2012. Systematics: A Course of Lectures. Wiley-Blackwell, Chichester.
44. Wheeler, W.C., 2014. Maximum a posteriori probability assignment (MAP-A): an optimality criterion for phylogenetic trees via weighting and dynamic programming. Cladistics, 30, 282-290.
45. Wheeler, W.C., Whiteley, P.M., 2014. Historical linguistics as a sequence optimization problem: the evolution and biogeography of Uto-Aztecan languages. Cladistics, 10.1111/cla.12078.
46. Wheeler, W.C., Gladstein, D.S., De Laet, J. 1996-2005. POY version 3.0. program and documentation available at http://research.amnh.org/scicomp/projects/poy.php (version 3.0.11). documentation by D. Janies and W. C. Wheeler. commandline documentation by J. De Laet and W. C. Wheeler. American Museum of Natural History, New York.
47. Wheeler, W.C., Lucaroni, N., Hong, L., Crowley, L., Varón, A. 2013. Poy 5.0. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php.