Research

High-performance computing at the AMNH has a nineteen-year history, beginning with homebrew clusters assembled by curators and graduate students. The computer clusters are used intensively for research that relies heavily on high-end capability computing in biology, genomics, astrophysics, and anthropology.

Projects

Anthropology

Network analysis of example Crow-Omaha and other kinship systems.

The Division of Anthropology at the AMNH has recently begun to rely on the use of tools more familiar in biological evolution and systematics due to advances in both data acquisition and databasing, and interpretive models based on a tree/network framework. The research of Anthropology curator Peter Whiteley employs an anthro-informatic approach, utilizing computational and phylogenetic tools to build on databases of human kinship variants, and test hypotheses about kinship system transformation and evolution.

Astrophysics

LH 95 stellar nursery in Large Magellanic Cloud. Credit: NASA/ESA.

Research in the Department of Astrophysics includes a major component of computational work. Led by Division Chair, Mordecai Mac Low, the group studies the formation of planets, and stars, and the effects of supernova explosions on interstellar gas, with applications to galactic winds and galaxy formation. They use numerical gas dynamical and magnetohydrodynamical (MHD) simulations as a primary tool.

Current Studies

  • Planet Formation
  • Turbulence in Protoplanetary disks
  • Star formation
  • Galactic Winds

Spotlight

Planet Formation

is believed to take place in the disks of gas and dust around forming stars. The earliest stages of that process occurs while the gas is moving through the disk and falling onto the star. This is known as accretion, and while we can observe it occurring, we do not have good theoretical insight into what is causing it. The most promising agent of accretion is turbulence driven by the magnetorotational instability. This turbulence is critical in understanding the dynamics of the gas and dust, the latter of which creates the seeds for planet formation. We are using the parallel computing facility at AMNH to make detailed turbulence models under a variety of conditions that might occur in protoplanetary disks. Having a medium sized facility--larger than a standard workstation but smaller than the largest supercomputers--allows us to make many, many small scale models. This in turn allows us to explore the parameter space before investing significant amounts of time on the largest supercomputing facilities.

-Jeff Oishi

Systematic Biology

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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.

Download

Current version: 2.7

Binaries

Source code

Documentation

Test files

POY

This site has been moved. We apologise for the inconvenience. The new site is located at, http://www.amnh.org/our-research/computational-sciences.


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Download

This site has been moved. We apologise for the inconvenience. The new site is located at, http://www.amnh.org/our-research/computational-sciences.


This page will redirect, if possible. Otherwise browse with the link above.

Old versions of POY

Version 4.1.1 (23 January 2009)

Citation

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

Binaries

Source code

Documentation

Version 4.1 (15 November 2008)

Citation

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

Binaries

Source code

Documentation

Version 4.0.2911 (7 October 2008)

Citation

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

Binaries

Source code

Documentation

Version 4.0.2885 (15 August 2008)

Citation

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

Binaries

Source code

Documentation

Version 4.0.2870 (21 May 2008)

Citation

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

Binaries

Source code

Documentation

Version 4.0 Beta build 2635 (11 March 2008)

Citation

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

Binaries

Source code

Documentation

Version 4.0 Beta build 2602 (8 February 2008)

Citation

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

Binaries

Source code

Documentation

Version 4.0 Beta build 2398 (23 October 2007)

Citation

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

Binaries

Source code

Documentation

Version 4.0 Beta build 2318 (12 October 2007)

Citation

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

Binaries

Source code

Documentation

Version 4.0 Beta build 2205 (10 September 2007)

Citation

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

Binaries

Source code

Documentation

Version 4.0 Beta build 1983 (18 July 2007)

Citation

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

Binaries

Source code

Documentation

Version 4.0 Beta build 1908 (12 June 2007)

Citation

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

Binaries

Source code

Documentation

Version 4.0 Beta build 1902 (11 June 2007)

Citation

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

Binaries

Source code

Documentation

Version 4.0 Beta build 1724 (29 March 2007)

Citation

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

Binaries

Source code

Documentation

Version 4.0 Beta build 1665 (17 February 2007)

Citation

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

Binaries

Source code

Documentation

Version 3.0.11

Binaries

Source code

Documentation

Related software

Version 3.0

Binaries

Source code

Documentation

Related software

Version 2.7

Binaries

Source code

Documentation

Version 2.0

Binaries

Source code

Documentation

Sample Files

Sample data for DOS

Sample data for Linux

Sample matrices

Sample output

Utilities

jack2hen

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

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.

 

Publications

Empirical and theoretical papers in astrophysics and biological sciences are listed in reverse chronological order on the following pages, and may be downloaded by clicking on each reference. In doing so, you agree to comply with United States copyright law (Title 17, United States Code), such that the reprints are not to be "used for any purpose other than private study, scholarship, or research."

Astrophysics

Empirical and theoretical papers in astrophysics and biological sciences are listed in reverse chronological order, and may be downloaded by clicking on each reference. In doing so, you agree to comply with United States copyright law (Title 17, United States Code), such that the reprints are not to be "used for any purpose other than private study, scholarship, or research."

Li, Y., Mac Low, M.-M., and Klessen, R.S. 2006. Star formation in isolated disk galaxies. II. Schmidt laws and star formation efficiency. Astrophys. J. 639: 879-896.

Oishi, J.S., and Mac Low, M.-M. 2006. The inability of ambipolar diffusion to set a characteristic mass scale in molecular clouds. Astrophys. J. 638: 281-285.

Jappsen, A.-K., Klessen, R.S., Larson, R.B., Li, Y., and Mac Low, M.-M. 2005. The stellar mass spectrum from non-isothermal gravoturbulent fragmentation. Astron. and Astrophys. 435: 611-623.

Hurley, J.R., Pols, O.R., Aarseth, S.J., and Tout, C.A. 2005. A complete N-body model of the old open cluster M67. MNRAS 363: 293-314.

Li, Y., Mac Low, M.-M., and Klessen, R.S. 2005b. Star formation in isolated disk galaxies. I. Models and characteristics of nonlinear gravitational collapse. Astrophys. J. 626: 823-843.

Li, Y., Mac Low, M.-M., and Klessen, R.S. 2005a. Control of star formation in galaxies by gravitational instability. Astrophys. J. Letters 620: L19-L22.

Li, Y., Mac Low, M.-M., and Abel, T. 2004b. Initial ionization of compressible turbulence. Astrophys. J. 610: 339-350.

Li, P.S., Norman, M.L., Mac Low, M.-M., and Heitsch, F. 2004c. The formation of self-gravitating cores in turbulent magnetized clouds. Astrophys. J. 605: 800-818.

Hurley, J.R., Tout, C.A., Aarseth, S.J., and Pols, O.R. 2004. Metallicity effects on open cluster dynamics. MNRAS 355: 1207-1216.

Fujita, A., Mac Low, M.-M., Ferrara, A., and Meiksin, A. 2004. Cosmological feedback from high-redshift dwarf galaxies. Astrophys. J. 613: 159-179.

Li, Y., Mac Low, M.-M., and Klessen, R.S. 2004a. Formation of globular clusters in galaxy mergers. Astrophys. J. Letters 614: L29-L32.

Li, Y., Klessen, R.S., and Mac Low, M.-M. 2003. The formation of stellar clusters in turbulent molecular clouds: Effects of the equation of state. Astrophys. J. 592: 975-985.

Hurley, J.R., and Shara, M.M. 2003. White dwarf sequences in dense star clusters. Astrophys. J. 589: 179-198.

Fujita, A., Martin, C., Mac Low, M.-M., and Abel, T. 2003. The influence of supershells and galactic outflows on the escape of ionizing radiation from dwarf starburst galaxies. Astrophys. J. 599: 50-69.

Fujita, A., Martin, C., Mac Low, M.-M., and Abel, T. 2003. Cosmological feedback from high-redshift dwarf galaxies. Astrophys. J. 599: 50-69.

Shara, M.M., Hurley, J.R. 2002. Star clusters as Type Ia supernova factories. Astrophys. J. 571: 830-842.

Hurley, J.R., and Shara, M.M., 2002b. The promiscuous nature of stars in clusters. Astrophys. J. 570:184-189.

Hurley, J.R., Shara, M.M. 2002a. Free-floating planets in stellar clusters: Not so surprising. Astrophys. J. 565: 1251-1256.

Biological sciences

Empirical and theoretical papers in astrophysics and biological sciences are listed in reverse chronological order, and may be downloaded by clicking on each reference. In doing so, you agree to comply with United States copyright law (Title 17, United States Code), such that the reprints are not to be "used for any purpose other than private study, scholarship, or research."

Wheeler, W.C. , L. Aagesen, C. P. Arango, J. Faivovich, T. Grant, C. D'Haese, D. Janies, W. L. Smith, A. Varón, and G. Giribet. 2006. Dynamic Homology and Phylogenetic Systematics: A Unified Approach Using POY. American Museum of Natural History, New York. 365 pp.

Vinh, L. S., A. Varón, and W. C. Wheeler. 2006. Pairwise alignment with rearrangement. Genome Informatics 17(2):141-151.

Smith, W.L. and W. C. Wheeler. 2006. Venom evolution widespread in fishes: a phylogenetic road map for the bioprospecting of piscine venoms. Journal of Heredity 97: 206-217.

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.

Wheeler, W.C. , M.J. Ramírez, L. Aagesen, and S. Schulmeister, 2006. Partition-free congruence analysis. Cladistics 22: 256-263.

Wheeler, W.C. 2006. Dynamic homology and the likelihood criterion. Cladistics 22: 157-170.

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.

Jansen, G., S. Devaere, P.H.H. Weekers, and D. Adriaens. 2006. Phylogenetic relationships and divergence time estimate of African anguilkliform catfish (Siluriformes: Clariidae) inferred from ribosomal gene and spacer sequences. Molecular Phylogenetics and Evolution 38: 65-78.

Schelly, R., W. Salzburger, S. Koblmuller, N. Duftner, and C. Sturmbauer. 2006. Phylogenetic relationships of the lamprologine cichlid genus Lepidiolamprologus (Teleostei: Perciformes) based on mitochondrial and nuclear sequences, suggesting introgressive hybridization. Molecular Phylogenetics and Evolution 38: 426-438.

Pickett, K.M., G.L. Tolman, W.C. Wheeler, and J.W. Wenzel. 2005. Parsimony overcomes statistical inconsistency with the addition of more data from the same gene. Cladistics 21: 438-445.

Aagesen, L. 2005. Direct optimization, affine gap costs, and node stability. Molecular Phylogenetics and Evolution 36: 641-653.

Aagesen, L., G. Petersen, and O. Seberg. 2005. Sequence length variation, indel costs, and congruence in sensitivity analysis. Cladistics 21: 15-30.

Prendini, L., P. Weygoldt, and W.C. Wheeler. 2005. Systematics of the Damon variegatus group of African whip spiders (Chelicerata: Amblypygi): Evidence from behaviour, morphology and DNA. Organisms Diversity & Evolution 5: 203-236.

Brito, P.H. 2005. The influence of Pleistocene glacial refugia on tawny owl genetic diversity and phylogeography in western Europe. Molecular Ecology 14: 3077-3094.

Wheeler, W. C. 2005. “Alignment, Dynamic Homology, and Optimization.” pp71-80 in Parsimony, Phylogeny, and Genomics. V. A. Albert eds. Oxford University Press, Oxford.

Sparks, J.S., P.V. Dunlap, and W.L. Smith. 2005. Evolution and diversification of a secually dimorphic luminescent system in ponyfishes (Teleostei: Leiognathidae), including diagnoses for two new genera. Cladistics 21: 305-327.

Faivovich, J., Haddad, C. F. B., Garcia, P. C. A., Frost, D. R., Campbell, J. A., and Wheeler, W. C., 2005. Systematic review of the frog family Hylidae, with special reference to Hylinae: Phylogenetic analysis and taxonomic revision. Bulletin of the American Museum of Natural History 294: 1-240.

Giribet G, Richter, S., Edgecombe G. D, and Wheeler W.C. 2005. “The position of crustaceans within the Arthopoda—evidence form nine molecular loci and morphology.” Pp. 307-352 in Crustacea and Arthropod Relationships, S. Koenemann and R. A. Jenner eds. Taylor and Franscis, Boca Raton.

Sparks, J.S., and W.L. Smith. 2004a. Phylogeography and biogeography of cichlid fishes (Teleostei: Perciformes: Cichlidae). Cladistics 20: 501-517.

Sparks, J.S., and W.L. Smith. 2004b. Phylogeny and biogeography of the Malagasy and Australian rainbowfishes (Teleostei: Melanotaenioidei): Gondwanan vicariance and evolution in freshwater. Mol. Phyl. Evol. 33: 719-734.

Giribet G, Edgecombe G. D., Carpenter J.M., d‘Haese C., Wheeler W.C. 2004. Is Ellipura monophyletic? A combined analysis of basal hexapod relationships with emphasis on the origin of insects. Organisms, Diversity, and Evolution 4:319-340.

Smith, W. L., and W. C. Wheeler. 2004. Polyphyly of the mail-cheeked fishes (Teleostei: Scorpaeniformes): evidence from mitochondrial and nuclear sequence data, Mol. Phyl. Evol. 32:627-646.

Faivovich, J., P. C. A. Garcia, F. Ananias, L. Lanari, N. G. Basso, and W.C. Wheeler. 2004. A molecular perspective on the phylogeny of the Hyla pulchella species group (Anura: Hylidae). Mol. Phyl. Evol, 32:938-950.

Wheeler, W. C., G. Giribet, and G. D. Edgecombe. 2004. “Arthropod Systematics: The Comparative Study of Genomic, Anatomical, and Paleontological Information.” pp. 281-295, Assembling the Tree of Life. J. Cracraft and M. J. Donoghue eds. Oxford University Press, Oxford.

Wheeler, W. C., D. Janies, and J. De Laet. 2004. “DNA sequence alignment and parallel processing.” in 2004 McGraw-Hill Yearbook of Science & Technology.

Schulmeister, D. and W. C. Wheeler. 2004. Phylogenetic analysis of developmental sequence heterochrony: an application of search-based character optimization. Evolution and Development, 6:50-57.

Asher, R.J., I. Horovitz, and M.R. Sanchez-Villagra. 2004. First combined cladistic analysis of marsupial mammal interrelationships. Molecular Phylogenetics and Evolution 33: 240-250.

Wheeler, W. C. 2003. Search-Based Optimization. Cladistics, 19:348-355.

Wheeler, W. C. 2003. Implied Alignment: A Synapomorphy-Based Mulitple Sequence Alignment Method. Cladistics, 19:261-268.

 

Wheeler, W. C. 2003. Iterative pass optimization. Cladistics, 19:254-260.

Norell, M. A., and W. C. Wheeler. 2003. Missing entry replacement data analysis: a statistical approach to dealing with missing data in paleontological and total evidence data sets. J. Vert. Paleont. 23:275-283.

Prendini, L., Crowe, T.M., and Wheeler, W.C. 2003. The family Scorpionidae Latreille, 1802: Phylogeny, taxonomy and biogeography. Invertebrate Systematics, 17:185-259.

Asher, R.J., M.J. Novacek, and J.H. Geisler. 2003. Relationships of endemic African mammals and their fossil relatives based on morphological and molecular evidence. Journal of Mammalian Evolution 10: 131-164.

Wheeler, W. C. 2002. “Optimization Alignment: Down, Up, Error, and Improvements.” Pp. 55-69. in R. Desalle, G. Giribet and W. Wheeler eds. Techniques in Molecular Systematics and Evolution. Birkhäuser Verlag, Basel Switzerland.

Wheeler, W. C., G. Giribet, and G. D. Edgecombe. 2002. “Arthropods.” In Encyclopedia of Evolution, Mark Pagel ed.. Oxford University Press.

Girbet, G., and W. C. Wheeler. 2002. On bivalve phylogeny: a high-level phylogeny of the mollusk class Bivalvia based on a combined analysis of morphology and DNA sequence data. Inv. Biol 121:271-324.

Janies, D. and W. C. Wheeler. 2002. “Theory and practice of parallel direct optimization.” pp. 115-124 in R. Desalle, G. Giribet and W. Wheeler eds. Molecular Systematics and Evolution: Theory and Practice. Birkhäuser Verlag, Basel Switzerland.

Edgecombe, G. D., G. Giribet, and W. C. Wheeler. 2002. Phylogeny of Henicopidae (Chilopoda: Lithobiomorpha): A combined analysis of morphology and five molecular loci. Syst. Ent.27:31-64.

Giribet, G., R. DeSalle, and W. C. Wheeler. 2002. “Pluralism” and the aims of phylogenetic analysis.” pp. 141-146 in R. Desalle, G. Giribet and W. Wheeler eds. Molecular Systematics and Evolution: Theory and Practice. Birkhäuser Verlag, Basel Switzerland.

Giribet, G., W. C. Wheeler, G. D. Edgecombe, and C. Babbitt. 2002. Phylogeny and systematic position of Opiliones: a combined analysis of chelicerate relationships using morphological and molecular data. Cladistics, 18:5-70.

Giribet, G., W. C. Wheeler, and J. Muona. 2002. “DNA multiple sequence alignments.” pp107-114 in R. Desalle, G. Giribet and W. Wheeler eds. Molecular Systematics and Evolution: Theory and Practice. Birkhäuser Verlag, Basel Switzerland.

Schulmeister, S., Wheeler, W. C., and Carpenter, J. M. 2002. Simultaneous analysis of basal Hymenoptera (Insecta) using sensitivity analysis. Cladistics 18:455-484.

Wheeler, W. C. 2001. “Homology and DNA sequence data.” Pp. 303-318. in G.P. Wagner ed. The Character Concept in Evolutionary Biology. Academic Press, New York. 622 pp.

Wheeler, W. C. 2001. Homology and the optimization of DNA sequence data. Cladistics, 17:S3-S11.

Wheeler , W. C., M. F. Whiting, J. C. Carpenter, and Q. D. Wheeler. 2001. “The phylogeny of the insect orders.” Cladistics, 12:1-57.

Frost, D.R., D. Janies, P.l.F. Mouton, and T.A. Titus. 2001. A molecular perspective on the phylogeny of the girdles lizards (Chordylidae, Squamata). American Museum Novitates 3310: 1–10.

Frost, D.R., M.T. Rodrigues, T. Grant, and T.A. Titus. 2001. Phylogenetics of the lizard genus Tropidurus (Squamata: Tropiduridae: Tropidurinae): Direct optimization, descriptive efficiency, and sensitivity analysis of congruence between molecular data and morphology. Molecular Phylogenetics and Evolution 21: 352–371.

Frost, D.R., R. Etheridge, D. Janies, and T.A. Titus. 2001. Total evidence, sequence alignment, evolution of polychrotid lizards, and a reclassification of the Iguania (Squamata: Iguania). American Museum Novitates 3343: 1–38.

Giribet, G and W. C. Wheeler. 2001. Some unusual small-subunit ribosomal DNA sequences of metazoans. American Museum Novitates., 3337:1-14.

Janies, D., and W. Wheeler. 2001. Efficiency of parallel direct optimization. Cladistics, 17:S71-S82.

Janies, D. 2001. Phylogenetic relationships of extant echinoderm classes. Canadian Journal of Zoology 79: 1232–1250.

Giribet, G., G. D. Edgecombe, and W. C. Wheeler. 2001. Arthropod phylogeny based on eight molecular loci and morphology. Nature 413: 157-161.

Giribet, G., D. L. Distel, M. Polz, W. Sterrer, and W. C. Wheeler. 2000. “Triploblastic relationships with emphasis on the acoelomates, and the position of Gnathostomulida, Cycliophora, Platyhelminthes, and Chaetognatha; a combined approach of 18S rDNA and Morphology.” Systematic Biology, 49:539-562.

Phillips, A., D. Janies, and W. C. Wheeler. 2000. “Multiple sequence alignment in phylogenetic analysis.” Mol. Phyl. Evol. 16:317-330.

Wheeler, W. C. 2000. Heuristic Reconstruction of Hypothetical-Ancestral DNA Sequences: Sequence Alignment versus Direct Optimization. Pp. 106-113. in R. Scotland and R. T. Pennington eds. Homology and Sytematics. Systematics Society, London. 217 pp.

Bang, R., R. DeSalle, and W. C. Wheeler. 2000. “Transformationalism, taxism and the role of developmental biology in systematics.” Sys. Biol, 49:19-27.

Edgecombe, G. D., Gonzalo Giribet and Ward Wheeler. 1999. “Phylogeny of Chilopoda: combining 18s and 28s rDNA sequences and morphology.” Pp. 293-331. In: Evolución y filogenia de Arthropoda (A. Melic, ed.). Sociedad Entomológica Aragonesa.

Giribet, G., G. D. Edgecombe, y W. C. Wheeler. 1999. “Sistemática y Filogenia de Artrópodos; estado de la cuestión con énfasis en análisis de datos moleculares.” In: Evolución y filogenia de Arthropoda (A. Melic, ed.). Sociedad Entomológica Aragonesa.

Carpenter, J. M., and W. C. Wheeler. 1999. “Numerical Cladistics, Simultaneous Analysis and Hexapod Phylogeny.” In: Evolución y filogenia de Arthropoda (A. Melic, ed.). Sociedad Entomológica Aragonesa.

Wheeler, W. C. 1999. “Fixed Character States and the Optimization of Molecular Sequence Data.” Cladistics 15: 379-385.

Wheeler, W. 1999. “Measuring topological congruence by extending character techniques.” Cladistics, 15:131-135.

Carpenter, J. M. and W. C. Wheeler. 1999. “Towards simultaneous analysis of morphological and molecular data in Hymenoptera.” Zoologica Scripta 28:251-260.

Giribet, G and W. C. Wheeler. 1999. “The position of arthropods in the animal kingdom: Ecdysozoa, islands, trees and the ‘parsimony ratchet.’” Molecular Phylogenetics and Evolution, 10:1-5.

Giribet, G and W. C. Wheeler. 1999. “On Gaps.” Molecular Phylogenetics and Evolution, 13:132-143.

Janies, D., and R. Mooi. 1998. Xyloplax is an asteroid. In M. Candia Carevali, and F. Bonasoro (eds), Echinoderm Research 1998. A. A. Balkema, Rotterdam, Netherlands, pp. XX–XX.

Wheeler, W. C. 1998. “Alignment Characters, Dynamic Programming, and Heuristic Solutions” pp. 243-251 in R. DeSalle, B. Schierwater, eds. Molecular Approaches to Ecology and Evolution 2nd Edition. Birkhäuser Verlag, Basel Switzerland.

Wheeler, W. C. 1998. “Molecular systematics and Arthropods.” Pp. 9-32. in G. D. Edgecombe ed. Arthropod Fossils and Phylogeny, Columbia University Press, New York.

Wheeler, W. C. and C. Y. Hayashi. 1998. “The phylogeny of the extant chelicerate orders.” Cladistics 14:173-192.

Wheeler, W. C. 1998. “Sampling, groundplans, total evidence and the systematics of arthropods.” Pp. 87-96. in R. A. Fortey and R. H. Thomas eds. Arthropod Relationships. Chapman and Hall, London.

Gladstein, D. S. and W. C. Wheeler. 1997-2002. “POY: The Optimization of Alignment Characters.” Program and Documentation. New York, NY. Available at ftp.amnh.org/pub/molecular. Documentation by D. Janies and W. C. Wheeler.

Whiting, M. F., J. C. Carpenter, Q. D. Wheeler, and W. C. Wheeler. 1997. “The Strepsiptera problem: phylogeny of the holometabolous insect orders inferred from 18S and 28S ribosomal DNA sequences and morphology.” Syst. Biol. 46:1-68.

Wheeler, W. C. 1996. “Optimization Alignment: the end of multiple sequence alignment in phylogenetics?” Cladistics, 12:1-9.

Vrana, P. B. and W. C. Wheeler. 1996. “Molecular evolution and phylogenetic utility of the Polyubiquitin locus in mammals and higher vertebrates.” Mol. Phyl. and Evol., 6:259-269.

Wheeler, W. C. 1995. “Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data.” Systematic Biology 44:321-331.

Wheeler, W. C., J. Gatesy, and R. DeSalle. 1995. “Elision: a method for accommodating multiple molecular sequence alignments with alignment-ambiguous sites.” Mol. Phyl. Evol.4:1-9.

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