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Computational problems in molecular systematics

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Molecular Ecology and Evolution: Approaches and Applications

Part of the book series: Experientia Supplementum ((EXS,volume 69))

Summary

The development of extremely powerful computer programs and the ready availability of microcomputers has revealed several computational problems with data analysis. These problems occur in the handling of systematic data in general and molecular systematic data in particular. This paper examines three areas of controversy in molecular systematics resulting from increased computer power. We start by examining the first step in DNA sequence analysis, the establishment of homology via sequence alignment. Next we examine several problems in phylogenetic analysis that have arisen in the last few years due to use of the PAUP (Swofford, 1991), HENNIG86 (Farris, 1988), and PHYLIP programs. These problems include limitations on the number of taxa examined in a given analysis and the accuracy of the parsimony trees in such analyses. The final subject is an examination of programs used for assessing tree robustness. We concentrate on certain programs (such as MALIGN (Wheeler and Gladstein, 1993), PAUP (Swofford, 1991), HENNIG86 (Farris, 1988), PHYLIP (Felsenstein, 1990), CLADOS (Nixon, 1993), MacClade (Maddison and Maddison, 1993), etc.), but similar comments about other programs could also be made.

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Authors and Affiliations

  1. Department of Entomology, American Museum of Natural History, New York, NY, 10024, USA

    R. DeSalle

  2. Department of Geology and Geophysics, Yale University, New Haven, CT, 06511, USA

    C. Wray

  3. Department of Biology, Yale University, New Haven, CT, 06511, USA

    R. Absher

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  1. R. DeSalle
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  2. C. Wray
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  3. R. Absher
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Editors and Affiliations

  1. Zoologisches Institut, Universität Frankfurt, Siesmayerstr. 70, D-60054, Frankfurt, Germany

    B. Schierwater  & B. Streit  & 

  2. Department of Biology, Yale University, 165 Prospect St., New Haven, CT, 06511, USA

    G. P. Wagner

  3. Department of Entomology, American Museum of Natural History, 79th Street at Central Park West, New York, NY, 10024, USA

    R. DeSalle

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DeSalle, R., Wray, C., Absher, R. (1994). Computational problems in molecular systematics. In: Schierwater, B., Streit, B., Wagner, G.P., DeSalle, R. (eds) Molecular Ecology and Evolution: Approaches and Applications. Experientia Supplementum, vol 69. Birkhäuser, Basel. https://doi.org/10.1007/978-3-0348-7527-1_21

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  • DOI: https://doi.org/10.1007/978-3-0348-7527-1_21

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