VESPA: Very large-scale Evolutionary and Selective Pressure Analyses
- Published
- Accepted
- Subject Areas
- Bioinformatics, Computational Biology
- Keywords
- Selective pressure analysis, protein molecular evolution, Large-scale comparative genomics, Gene family evolution, Positive selection
- Copyright
- © 2017 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
- 2017. VESPA: Very large-scale Evolutionary and Selective Pressure Analyses. PeerJ Preprints 5:e1895v2 https://doi.org/10.7287/peerj.preprints.1895v2
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
We have updated all the remaining text based errors (typos) and have updated the figures as requested. We addressed all issues raised and thank the editor for their valuable feedback in improving this manuscript.
Supplemental Information
VESPA User Manual
Detailed manual containing all instructions for use of VESPA.