Access

You are not currently logged in.

Access your personal account or get JSTOR access through your library or other institution:

login

Log in to your personal account or through your institution.

The PhyLoTA Browser: Processing GenBank for Molecular Phylogenetics Research

Michael J. Sanderson, Darren Boss, Duhong Chen, Karen A. Cranston and Andre Wehe
Systematic Biology
Vol. 57, No. 3 (Jun., 2008), pp. 335-346
Stable URL: http://www.jstor.org/stable/27756352
Page Count: 12
  • Download ($42.00)
  • Cite this Item
The PhyLoTA Browser: Processing GenBank for Molecular Phylogenetics Research
Preview not available

Abstract

As an archive of sequence data for over 165,000 species, GenBank is an indispensable resource for phylogenetic inference. Here we describe an informatics processing pipeline and online database, the PhyLoTA Browser (http://loco.biosci.arizona.edu/pb), which offers a view of GenBank tailored for molecular phylogenetics. The first release of the Browser is computed from 2.6 million sequences representing the taxonomically enriched subset of GenBank sequences for eukaryotes (excluding most genome survey sequences, ESTs, and other high-throughput data). In addition to summarizing sequence diversity and species diversity across nodes in the NCBI taxonomy, it reports 87,000 potentially phylogenetically informative clusters of homologous sequences, which can be viewed or downloaded, along with provisional alignments and coarse phylogenetic trees. At each node in the NCBI hierarchy, the user can display a "data availability matrix" of all available sequences for entries in a subtaxa-by-clusters matrix. This matrix provides a guidepost for subsequent assembly of multigene data sets or supertrees. The database allows for comparison of results from previous GenBank releases, highlighting recent additions of either sequences or taxa to GenBank and letting investigators track progress on data availability worldwide. Although the reported alignments and trees are extremely approximate, the database reports several statistics correlated with alignment quality to help users choose from alternative data sources.

Page Thumbnails

  • Thumbnail: Page 
335
    335
  • Thumbnail: Page 
336
    336
  • Thumbnail: Page 
337
    337
  • Thumbnail: Page 
338
    338
  • Thumbnail: Page 
339
    339
  • Thumbnail: Page 
340
    340
  • Thumbnail: Page 
341
    341
  • Thumbnail: Page 
342
    342
  • Thumbnail: Page 
343
    343
  • Thumbnail: Page 
344
    344
  • Thumbnail: Page 
345
    345
  • Thumbnail: Page 
346
    346