VESPA: Very large-scale Evolutionary and Selective Pressure Analyses

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1 Bioinformatics and Molecular Evolution Group, School of Biotechnology, Faculty of Science and Health, Dublin City University, Dublin 9, Ireland
2 Computational and Molecular Evolutionary Biology, School of Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, United Kingdom
DOI
10.7287/peerj.preprints.1895v1
Published
Accepted
Subject Areas
Bioinformatics, Computational Biology
Keywords
Selective pressure analysis, protein molecular evolution, Large-scale comparative genomics, Gene family evolution, Positive selection
Copyright
© 2016 Webb et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Webb AE, Walsh TA, O'Connell MJ. 2016. VESPA: Very large-scale Evolutionary and Selective Pressure Analyses. PeerJ Preprints 4:e1895v1

Abstract

Large-scale molecular evolutionary analyses of protein coding sequences requires a number of preparatory inter-related steps from finding gene families, to generating alignments and phylogenetic trees and assessing selective pressure variation. Each phase of these analyses can represent significant challenges particularly when working with the entire genome of large sets of species. We present VESPA, software capable of automating a selective pressure analysis using codeML in addition to the preparatory analyses and summary statistics. VESPA is written in python and is designed to run within a UNIX environment. Large-scale gene family identification, sequence alignment, and phylogeny reconstruction are all important aspects of large-scale molecular evolutionary analyses. VESPA provides flexible software for simplifying these processes along with downstream selective pressure variation analyses. The software automatically interprets results from codeML and produces simplified summary files to assist the user in better understanding the results. VESPA may be found at the following website: www.mol-evol.org/VESPA

Author Comment

This is a submission to PeerJ Computer Science for review.

Supplemental Information

VESPA User Manual

Detailed manual containing all instructions for use of VESPA.

DOI: 10.7287/peerj.preprints.1895v1/supp-1