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Related Experiment Video

Updated: Jun 23, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Berkeley PHOG: PhyloFacts orthology group prediction web server.

Ruchira S Datta¹, Christopher Meacham, Bushra Samad

¹QB3 Institute, University of California, Berkeley, CA, USA. ruchira@berkeley.edu

Nucleic Acids Research

|May 14, 2009

Summary

The PHOG web server uses a novel phylogenetic algorithm for accurate ortholog detection. It offers high recall and precision, outperforming existing tools like InParanoid and OrthoMCL.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Ortholog detection is crucial for genome functional annotation.
Applications include phylogenetic analysis and protein interaction prediction.

Purpose of the Study:

Introduce the PHOG web server for ortholog identification.
Utilize a novel algorithm based on phylogenetic analysis.

Main Methods:

Developed a new algorithm for ortholog detection using phylogenetic analysis.
Benchmarked performance against InParanoid and OrthoMCL using TreeFam-A data.
Incorporated tree-distance thresholds for adjustable precision and recall.

Main Results:

PHOG demonstrates competitive recall and precision compared to InParanoid and OrthoMCL.
PHOG achieves higher recall at comparable precision levels.
A high-recall PHOG variant significantly improves precision over InParanoid.

Conclusions:

PHOG is an effective tool for ortholog detection with tunable parameters.
The PHOG web server provides access to over 366K orthology groups.
Results are linked to functional annotations and biological literature.