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CAAStools: a toolbox to identify and test Convergent Amino Acid Substitutions

MOTIVATION: Coincidence of Convergent Amino Acid Substitutions (CAAS) with phenotypic convergences allow pinpointing genes and even individual mutations that are likely to be associated with trait variation within their phylogenetic context. Such findings can provide useful insights into the genetic...

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Detalles Bibliográficos
Autores principales: Barteri, Fabio, Valenzuela, Alejandro, Farré, Xavier, de Juan, David, Muntané, Gerard, Esteve-Altava, Borja, Navarro, Arcadi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10598582/
https://www.ncbi.nlm.nih.gov/pubmed/37846039
http://dx.doi.org/10.1093/bioinformatics/btad623
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author Barteri, Fabio
Valenzuela, Alejandro
Farré, Xavier
de Juan, David
Muntané, Gerard
Esteve-Altava, Borja
Navarro, Arcadi
author_facet Barteri, Fabio
Valenzuela, Alejandro
Farré, Xavier
de Juan, David
Muntané, Gerard
Esteve-Altava, Borja
Navarro, Arcadi
author_sort Barteri, Fabio
collection PubMed
description MOTIVATION: Coincidence of Convergent Amino Acid Substitutions (CAAS) with phenotypic convergences allow pinpointing genes and even individual mutations that are likely to be associated with trait variation within their phylogenetic context. Such findings can provide useful insights into the genetic architecture of complex phenotypes. RESULTS: Here we introduce CAAStools, a set of bioinformatics tools to identify and validate CAAS in orthologous protein alignments for predefined groups of species representing the phenotypic values targeted by the user. AVAILABILITY AND IMPLEMENTATION: CAAStools source code is available at http://github.com/linudz/caastools, along with documentation and examples.
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spelling pubmed-105985822023-10-26 CAAStools: a toolbox to identify and test Convergent Amino Acid Substitutions Barteri, Fabio Valenzuela, Alejandro Farré, Xavier de Juan, David Muntané, Gerard Esteve-Altava, Borja Navarro, Arcadi Bioinformatics Applications Note MOTIVATION: Coincidence of Convergent Amino Acid Substitutions (CAAS) with phenotypic convergences allow pinpointing genes and even individual mutations that are likely to be associated with trait variation within their phylogenetic context. Such findings can provide useful insights into the genetic architecture of complex phenotypes. RESULTS: Here we introduce CAAStools, a set of bioinformatics tools to identify and validate CAAS in orthologous protein alignments for predefined groups of species representing the phenotypic values targeted by the user. AVAILABILITY AND IMPLEMENTATION: CAAStools source code is available at http://github.com/linudz/caastools, along with documentation and examples. Oxford University Press 2023-10-16 /pmc/articles/PMC10598582/ /pubmed/37846039 http://dx.doi.org/10.1093/bioinformatics/btad623 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Barteri, Fabio
Valenzuela, Alejandro
Farré, Xavier
de Juan, David
Muntané, Gerard
Esteve-Altava, Borja
Navarro, Arcadi
CAAStools: a toolbox to identify and test Convergent Amino Acid Substitutions
title CAAStools: a toolbox to identify and test Convergent Amino Acid Substitutions
title_full CAAStools: a toolbox to identify and test Convergent Amino Acid Substitutions
title_fullStr CAAStools: a toolbox to identify and test Convergent Amino Acid Substitutions
title_full_unstemmed CAAStools: a toolbox to identify and test Convergent Amino Acid Substitutions
title_short CAAStools: a toolbox to identify and test Convergent Amino Acid Substitutions
title_sort caastools: a toolbox to identify and test convergent amino acid substitutions
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10598582/
https://www.ncbi.nlm.nih.gov/pubmed/37846039
http://dx.doi.org/10.1093/bioinformatics/btad623
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