Webb, AE, Walsh, TA and O'Connell, MJ orcid.org/0000-0002-1877-1001 (2017) VESPA: Very large-scale Evolutionary and Selective Pressure Analyses. PeerJ Computer Science, 3. e118. ISSN 2376-5992
Abstract
Background: 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 entire proteomes (all protein coding sequences in a genome) from a large number of species. Methods: 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 Perl and is designed to run within a UNIX environment. Results: We have benchmarked VESPA and our results show that the method is consistent, performs well on both large scale and smaller scale datasets, and produces results in line with previously published datasets. Discussion: 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.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2017 Webb et al. 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 Computer Science) and either DOI or URL of the article must be cited. |
Keywords: | Selective pressure analysis, Protein molecular evolution, Large-scale comparative genomics, Gene family evolution, Positive selection |
Dates: |
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Institution: | The University of Leeds |
Academic Units: | The University of Leeds > Faculty of Biological Sciences (Leeds) > School of Biology (Leeds) |
Depositing User: | Symplectic Publications |
Date Deposited: | 13 Jun 2017 14:20 |
Last Modified: | 19 Mar 2018 12:18 |
Published Version: | https://doi.org/10.7717/peerj-cs.118 |
Status: | Published |
Publisher: | PeerJ |
Identification Number: | 10.7717/peerj-cs.118 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:117723 |