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Updated: Jun 20, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees.

Philippe Gouret¹, Julie D Thompson, Pierre Pontarotti

¹UMR 6632, Evolutionary Biology and Modeling, University of Provence, Marseille, France. philippe.gouret@univ-provence.fr

BMC Bioinformatics

|September 22, 2009

Summary

PhyloPattern is a new software library that automates phylogenetic tree analysis for evolutionary biology. It simplifies complex tasks like node annotation and pattern matching, accelerating research in genome-scale studies.

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Area of Science:

Computational Biology
Evolutionary Biology
Bioinformatics

Background:

Genome-scale studies require automated analysis of numerous phylogenetic trees.
Recognizing complex architectures within trees is crucial for information extraction.

Purpose of the Study:

To introduce PhyloPattern, a novel software library for automating phylogenetic tree manipulations and analysis.
To facilitate high-throughput phylogenetic tree analysis for evolutionary biology research.

Main Methods:

PhyloPattern offers three core modules: node annotation, pattern matching, and tree comparison.
It enables immediate or deferred evaluation of node properties using predefined or user-defined annotation functions.
The library supports searching for user-defined patterns in large phylogenetic trees and pairwise tree comparison.

Main Results:

PhyloPattern automates essential tasks in high-throughput phylogenetic tree analysis.
It allows programmers to focus on specific analytical aspects rather than low-level manipulations.
The software facilitates dynamic pattern generation for tree comparison.

Conclusions:

PhyloPattern significantly simplifies and accelerates computational work in evolutionary biology.
The library has been successfully applied to identify phylogenetic evidence for domain shuffling and gene loss.
Any workflow involving phylogenetic tree analysis can be automated using PhyloPattern.