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A Practical Guide to Phylogenetics for Nonexperts
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AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses.

Surendra Kumar1, Asmund Skjaeveland, Russell J S Orr

  • 1Microbial Evolution Research Group, Department of Biology, University of Oslo, Norway. surendra.kumar@bio.uio.no

BMC Bioinformatics
|October 30, 2009
PubMed
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The AIR program package aids phylogenomic analyses by creating multigene alignments and removing fast-evolving sites. This improves the accuracy and resolution of evolutionary trees, especially for early eukaryotes.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Large multigene sequence alignments are crucial for phylogenomic reconstruction of the eukaryote tree of life.
  • These supermatrices offer more information than single genes but also introduce noise from fast-evolving sites.
  • Reducing noise by removing fast-evolving sites is key to improving phylogenetic resolution.

Purpose of the Study:

  • To present AIR, a web-based program package for phylogenomic analyses.
  • To enable transformation of single genes into multigene alignments.
  • To identify evolutionary rates and remove fast-evolving sites from alignments.

Main Methods:

  • AIR comprises AIR-Appender, AIR-Identifier, and AIR-Remover for alignment processing.

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  • The package facilitates batch-oriented, web-based processing of sequence data.
  • It allows for semi-automated pipelines and independent use of its components.

    • Main Results:

    • AIR transforms multiple genes into a single multigene alignment.
    • It accurately identifies evolutionary rates within these alignments.
    • Fast-evolving sites are effectively removed, producing filtered alignments.

    Conclusions:

    • The AIR program package enhances the creation and analysis of multigene alignments.
    • Removing fast-evolving sites improves phylogenetic resolution and statistical support.
    • AIR has been successfully applied to studies of early diverging eukaryotes.