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Updated: Jul 15, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis.

Jake Gunn Glanville¹, Dan Kirshner, Nandini Krishnamurthy

¹Berkeley Phylogenomics Group, University of California, Berkeley, USA.

Nucleic Acids Research

|May 10, 2007

Summary

Phylogenomic analysis offers accurate protein molecular function prediction, overcoming annotation transfer limits. The Berkeley Phylogenomics Group provides web servers for integrated phylogenomic pipelines and analysis.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Protein function prediction is crucial in molecular biology.
Annotation transfer methods have limitations in accuracy.
Phylogenomic analysis offers a more accurate approach.

Purpose of the Study:

To present web servers for phylogenomic analysis.
To provide an integrated pipeline for protein sequence analysis.
To improve protein molecular function prediction accuracy.

Main Methods:

Utilizing the PhyloFacts Phylogenomic Encyclopedia for classification.
Employing FlowerPower for protein domain architecture clustering.
Using MUSCLE for multiple sequence alignment.
Implementing SATCHMO for simultaneous alignment and tree construction.
Applying SCI-PHY for subfamily identification.
Integrating these tools into the PhyloBuilder web server pipeline.

Main Results:

Phylogenomic analysis enables highly accurate protein molecular function prediction.
The Berkeley Phylogenomics Group offers a suite of specialized web servers.
The PhyloBuilder server provides a comprehensive, integrated analysis pipeline from sequence to structure prediction.

Conclusions:

Phylogenomic analysis is the most accurate method for predicting protein molecular function.
The provided web servers and pipeline offer valuable resources for researchers.
These tools facilitate in-depth analysis of protein sequences and functions.