VESPA: Very large-scale Evolutionary and Selective Pressure Analyses
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 s...
Main Authors: | , , |
---|---|
Format: | Article |
Language: | English |
Published: |
PeerJ Inc.
2017-06-01
|
Series: | PeerJ Computer Science |
Subjects: | |
Online Access: | https://peerj.com/articles/cs-118.pdf |
id |
doaj-1987e4ef116b49c1ac4ffa0c1419b929 |
---|---|
record_format |
Article |
spelling |
doaj-1987e4ef116b49c1ac4ffa0c1419b9292020-11-24T22:41:38ZengPeerJ Inc.PeerJ Computer Science2376-59922017-06-013e11810.7717/peerj-cs.118VESPA: Very large-scale Evolutionary and Selective Pressure AnalysesAndrew E. Webb0Thomas A. Walsh1Mary J. O’Connell2Bioinformatics and Molecular Evolution Group, School of Biotechnology, Faculty of Science and Health, Dublin City University, Dublin, IrelandBioinformatics and Molecular Evolution Group, School of Biotechnology, Faculty of Science and Health, Dublin City University, Dublin, IrelandBioinformatics and Molecular Evolution Group, School of Biotechnology, Faculty of Science and Health, Dublin City University, Dublin, IrelandBackground 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. VESPA may be found at the following website: http://www.mol-evol.org/VESPA.https://peerj.com/articles/cs-118.pdfSelective pressure analysisProtein molecular evolutionLarge-scale comparative genomicsGene family evolutionPositive selection |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Andrew E. Webb Thomas A. Walsh Mary J. O’Connell |
spellingShingle |
Andrew E. Webb Thomas A. Walsh Mary J. O’Connell VESPA: Very large-scale Evolutionary and Selective Pressure Analyses PeerJ Computer Science Selective pressure analysis Protein molecular evolution Large-scale comparative genomics Gene family evolution Positive selection |
author_facet |
Andrew E. Webb Thomas A. Walsh Mary J. O’Connell |
author_sort |
Andrew E. Webb |
title |
VESPA: Very large-scale Evolutionary and Selective Pressure Analyses |
title_short |
VESPA: Very large-scale Evolutionary and Selective Pressure Analyses |
title_full |
VESPA: Very large-scale Evolutionary and Selective Pressure Analyses |
title_fullStr |
VESPA: Very large-scale Evolutionary and Selective Pressure Analyses |
title_full_unstemmed |
VESPA: Very large-scale Evolutionary and Selective Pressure Analyses |
title_sort |
vespa: very large-scale evolutionary and selective pressure analyses |
publisher |
PeerJ Inc. |
series |
PeerJ Computer Science |
issn |
2376-5992 |
publishDate |
2017-06-01 |
description |
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. VESPA may be found at the following website: http://www.mol-evol.org/VESPA. |
topic |
Selective pressure analysis Protein molecular evolution Large-scale comparative genomics Gene family evolution Positive selection |
url |
https://peerj.com/articles/cs-118.pdf |
work_keys_str_mv |
AT andrewewebb vespaverylargescaleevolutionaryandselectivepressureanalyses AT thomasawalsh vespaverylargescaleevolutionaryandselectivepressureanalyses AT maryjoconnell vespaverylargescaleevolutionaryandselectivepressureanalyses |
_version_ |
1725701492275412992 |