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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan / Hassani-Pak, Keywan


CiteScore 2018: 0.90

SCImago Journal Rank (SJR) 2018: 0.315

Open Access
Online
ISSN
1613-4516
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Volume 9, Issue 3

Issues

ADOPS - Automatic Detection Of Positively Selected Sites

David Reboiro-Jato / Miguel Reboiro-Jato / Florentino Fdez-Riverola / Cristina P. Vieira
  • Instituto de Biologia Molecular e Celular, Universidade do Porto, http://www.ibmc.up.pt, Portugal
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Nuno A. Fonseca
  • CRACS-INESC Porto LA, Universidade do Porto, http://cracs.fc.up.pt/ United Kingdom of Great Britain and Northern Ireland
  • EMBL-European Bioinformatics Institute, http://www.ebi.ac.uk/, United Kingdom of Great Britain and Northern Ireland
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Jorge Vieira
  • Corresponding author
  • Instituto de Biologia Molecular e Celular, Universidade do Porto, http://www.ibmc.up.pt, Portugal
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2012-200

Summary

Maximum-likelihood methods based on models of codon substitution have been widely used to infer positively selected amino acid sites that are responsible for adaptive changes. Nevertheless, in order to use such an approach, software applications are required to align protein and DNA sequences, infer a phylogenetic tree and run the maximum-likelihood models. Therefore, a significant effort is made in order to prepare input files for the different software applications and in the analysis of the output of every analysis. In this paper we present the ADOPS (Automatic Detection Of Positively Selected Sites) software. It was developed with the goal of providing an automatic and flexible tool for detecting positively selected sites given a set of unaligned nucleotide sequence data. An example of the usefulness of such a pipeline is given by showing, under different conditions, positively selected amino acid sites in a set of 54 Coffea putative S-RNase sequences. ADOPS software is freely available and can be downloaded from http://sing.ei.uvigo.es/ADOPS.

About the article

Published Online: 2016-10-18

Published in Print: 2012-12-01


Citation Information: Journal of Integrative Bioinformatics, Volume 9, Issue 3, Pages 18–32, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2012-200.

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© 2012 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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