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TaxMan: a taxonomic database manager.

Martin Jones1, Mark Blaxter

  • 1Institute of Evolutionary Biology, King's Buildings, Ashworth Laboratories, West Mains Road, Edinburgh EH9 3JT, UK. martin.jones@ed.ac.uk

BMC Bioinformatics
|December 21, 2006
PubMed
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TaxMan software automates the assembly of large, aligned gene sequence datasets for phylogenetic analysis. This tool speeds up the process of building supermatrices, improving the efficiency of evolutionary studies.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Phylogenetic analysis using large, multi-gene datasets is crucial for resolving evolutionary relationships.
  • Manual assembly of these datasets is time-consuming and prone to errors.
  • Challenges include unrepresented, multiple, or partial gene sequences per species.

Purpose of the Study:

  • To develop a software package, TaxMan, for automating phylogenetic dataset assembly.
  • To facilitate the creation of large, aligned sequence datasets for phylogenetic studies.
  • To address the challenges of sequence acquisition, curation, and alignment.

Main Methods:

  • Utilizes freely available tools for sequence extraction from GenBank based on annotation and similarity.

Related Experiment Videos

  • Automates consensus sequence building and alignment, preferably at the protein level.
  • Stores aligned sequences in a database for rapid generation of concatenated multiple sequence alignments.

    • Main Results:

    • TaxMan enables rapid, automated assembly of multigene datasets for large taxonomic groups.
    • It ensures all available sequence data is utilized by considering both annotation and BLAST similarity.
    • The software assists in selecting optimal taxon subsets for phylogenetic analysis.

    Conclusions:

    • TaxMan significantly accelerates the generation of multiple sequence alignments for phylogenetic studies.
    • The automated phylogenetic workbench is effective when guided by user expertise.
    • It handles thousands of records efficiently, aiding complex evolutionary research.