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A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
The PhyLoTA Browser: processing GenBank for molecular phylogenetics research.
Michael J Sanderson1, Darren Boss, Duhong Chen
1Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA. sanderm@email.arizona.edu
Systematic Biology
|June 24, 2008
Summary
The PhyLoTA Browser offers a specialized view of GenBank sequence data for molecular phylogenetics. It identifies 87,000 homologous sequence clusters to aid phylogenetic inference and data set assembly.
Area of Science:
- Bioinformatics
- Computational Biology
- Molecular Phylogenetics
Background:
- GenBank is a crucial archive for biological sequence data, supporting over 165,000 species.
- Molecular phylogenetics relies heavily on comprehensive and accessible sequence data.
- Existing GenBank data requires specialized processing for efficient phylogenetic analysis.
Purpose of the Study:
- To introduce the PhyLoTA Browser, an informatics pipeline and online database.
- To provide a GenBank subset tailored for molecular phylogenetics research.
- To facilitate the identification and utilization of phylogenetically informative sequence clusters.
Main Methods:
- Developed an informatics processing pipeline and online database (PhyLoTA Browser).
- Processed 2.6 million eukaryotic sequences from GenBank, excluding high-throughput data.
- Summarized sequence and species diversity across NCBI taxonomy nodes.
Main Results:
- Identified 87,000 potentially phylogenetically informative clusters of homologous sequences.
- Generated provisional alignments and coarse phylogenetic trees for these clusters.
- Developed a "data availability matrix" to guide multigene data set assembly.
Conclusions:
- The PhyLoTA Browser enhances GenBank's utility for molecular phylogenetics.
- The database aids in tracking data availability and assembling phylogenetic datasets.
- Provides tools and statistics to assist users in selecting appropriate data sources for phylogenetic studies.
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