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A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction.

Jia-Ming Chang¹, Paolo Di Tommaso², Vincent Lefort³

¹Comparative Bioinformatics, Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain Institute of Human Genetics (IGH), UPR 1142, CNRS, 34396 Montpellier, France.

Nucleic Acids Research

|April 10, 2015

Summary

This summary is machine-generated.

This study presents the Transitive Consistency Score (TCS) web server for assessing protein multiple sequence alignment (MSA) reliability. It helps identify reliable alignment positions for structural analysis and accurate phylogenetic reconstruction.

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Area of Science:

Bioinformatics
Computational Biology
Structural Biology

Background:

Protein multiple sequence alignments (MSAs) are crucial for understanding protein evolution and function.
Assessing the reliability of MSAs is essential for downstream analyses like phylogenetic reconstruction and structural prediction.
Existing methods for MSA quality assessment and filtering have limitations.

Purpose of the Study:

To introduce the Transitive Consistency Score (TCS) web server, a novel tool for estimating the local reliability of protein MSAs.
To provide a method for identifying aligned positions that are likely to contain structurally analogous residues.
To offer a tool that aids in selecting reliable alignment regions for accurate phylogenetic tree reconstruction.

Main Methods:

The study introduces the Transitive Consistency Score (TCS) index.
A web server was developed to make the TCS index accessible for practical use.
The performance of TCS was evaluated against common MSA filtering methods.

Main Results:

The TCS index accurately predicts the correctness of structural alignments.
TCS outperforms established filtering schemes like Gblocks and trimAl in post-processing MSAs for phylogenetic analysis.
The TCS web server provides a reliable estimation of local MSA reliability.

Conclusions:

The TCS web server offers a valuable resource for the bioinformatics community.
Utilizing TCS can improve the accuracy of structural and phylogenetic analyses derived from MSAs.
TCS represents an advancement in assessing and improving the quality of protein MSAs.