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Updated: May 31, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees.

Brigitte Boeckmann¹, Marc Robinson-Rechavi, Ioannis Xenarios

¹Swiss Institute of Bioinformatics, Centre Médical Universitaire, 1211 Geneva 4, Switzerland. brigitte.boeckmann@isb-sib.ch

Briefings in Bioinformatics

|July 9, 2011

Summary

This summary is machine-generated.

Comparing seven phylogenomic databases revealed significant differences in orthology predictions. Most databases lack comprehensive and correct protein classifications, highlighting the need for standardized quality assessments.

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Area of Science:

Bioinformatics
Comparative Genomics
Evolutionary Biology

Background:

Phylogenomic databases offer orthology predictions for sequenced species.
Significant variations exist in the content and accuracy of these databases.

Purpose of the Study:

To systematically compare seven prominent ortholog databases.
To evaluate the accuracy and completeness of orthology assignments.

Main Methods:

Comparison of Ensembl Compara, eggNOG, HOGENOM, InParanoid, OMA, OrthoDB, and Panther.
Utilized reference trees for three well-conserved protein families.
Assessed specificity, completeness, and phylogenetic information.

Main Results:

High specificity of orthology assignments was generally observed.
Differences stemmed primarily from database concepts, not methodologies.
No single database provided a fully correct and comprehensive protein classification.

Conclusions:

A framework for systematic phylogenomic database comparison was established.
Standardized 'Gold standard' trees are needed for quality assessment and improvement.
Future efforts should focus on enhancing database accuracy and comprehensiveness.