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TreeFam: 2008 Update.

Jue Ruan1, Heng Li, Zhongzhong Chen

  • 1Beijing Institute of Genomics of the Chinese Academy of Sciences, Beijing Genomics Institute, Beijing 101300, China.

Nucleic Acids Research
|December 7, 2007
PubMed
Summary
This summary is machine-generated.

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TreeFam release 4.0 offers curated and automated phylogenetic trees for animal gene families, enhancing orthologue and paralogue assignments with expanded genomic data and improved methods for gene family analysis.

Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • The TreeFam database provides curated phylogenetic trees and orthologue/paralogue assignments for animal gene families.
  • Accurate gene family analysis is crucial for understanding evolutionary relationships.

Purpose of the Study:

  • To release TreeFam version 4.0 with expanded data and improved analytical methods.
  • To enhance the accuracy of gene family grouping, phylogenetic tree construction, and orthologue/paralogue inference.

Main Methods:

  • Incorporated 25 fully sequenced animal genomes and four outgroup species.
  • Developed refined algorithms for automatic gene family grouping and phylogenetic tree building.
  • Enhanced methods for inferring orthologous and paralangous relationships.

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Main Results:

  • Release 4.0 includes curated trees for 1,314 families and automated trees for 14,351 families.
  • Expanded genomic coverage and improved computational approaches increase the accuracy of gene family data.
  • The user interface and data accessibility via a Perl API have been upgraded.

Conclusions:

  • TreeFam 4.0 represents a significant advancement in providing comprehensive and accurate gene family data for evolutionary studies.
  • The enhanced database and tools facilitate deeper insights into animal gene evolution and function.