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BranchClust: a phylogenetic algorithm for selecting gene families.

Maria S Poptsova¹, J Peter Gogarten

¹Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125, USA. maria.poptsova@uconn.edu

BMC Bioinformatics

|April 12, 2007

Summary

BranchClust is a new algorithm for automated orthologous gene selection that accurately distinguishes orthologs from paralogs across any number of taxa. This method outperforms existing approaches like Reciprocal Best Blast hits for reliable gene family assembly.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Automated gene family assembly methods often struggle to differentiate orthologs from paralogs or are limited by the number of taxa.
Phylogenetic approaches require a known species tree, which is frequently unavailable, especially for prokaryotes.

Purpose of the Study:

To develop an automated algorithm for accurate orthologous gene selection.
To distinguish between complete and incomplete gene families and identify in- and outparalogs.

Main Methods:

Developed the BranchClust algorithm for automated orthologous gene identification using phylogenetic trees.
Implemented the algorithm in Perl utilizing BioPerl for tree parsing.
Algorithm handles any number of taxa and distinguishes gene family types.

Main Results:

BranchClust successfully identifies orthologous genes across diverse taxa.
The algorithm differentiates complete and incomplete gene families and recognizes in- and outparalogs.
Performance evaluation showed BranchClust surpasses the Reciprocal Best Blast hit method.

Conclusions:

BranchClust provides a more accurate method for selecting orthologous gene sets compared to existing techniques.
Manual inspection of phylogenetic trees validated the correctness of identified gene families and paralogs.