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AN EMPIRICAL COMPARISON OF MICROCOMPUTER PARSIMONY PROGRAMS.

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Two microcomputer programs, PHYLIP and PAUP, offer effective cladistic analysis, matching or exceeding older mainframe programs. While PHYLIP has efficiency issues, both can yield accurate, cost-effective solutions with modern computing.

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Area of Science:

  • Computational Biology
  • Systematics
  • Phylogenetic Analysis

Background:

  • Evaluating computational tools for phylogenetic analysis is crucial for systematic biology.
  • Microcomputer software offers potential for efficient and accessible cladistic analyses.
  • Previous benchmarks used mainframe programs, necessitating evaluation of newer microcomputer alternatives.

Purpose of the Study:

  • To assess the effectiveness and efficiency of microcomputer parsimony programs (PHYLIP, PAUP, SHEN).
  • To compare their performance against established mainframe programs using diverse datasets.
  • To determine their suitability for obtaining accurate and cost-effective cladistic solutions.

Main Methods:

  • Evaluation of three microcomputer parsimony programs: PHYLIP, PAUP, and a prototype SHEN.
  • Testing with 35 datasets, including those used for benchmarking mainframe programs.
  • Analysis of program accuracy, efficiency (computer time), and ability to detect multiple solutions.

Main Results:

  • Both PHYLIP and PAUP demonstrate effective performance, with accuracy comparable to or exceeding older mainframe programs.
  • PHYLIP exhibits lower efficiency and limitations in detecting multiple equally parsimonious solutions with heuristic algorithms.
  • Exact algorithms in PHYLIP and PAUP, while avoiding multiple solution detection issues, can generate excessive output.

Conclusions:

  • Microcomputer programs like PHYLIP and PAUP are effective tools for cladistic analysis.
  • Careful selection of program options enhances accuracy.
  • Advancements in computing suggest exact and cost-effective cladistic solutions are increasingly attainable.