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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...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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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. |
format | Online Article Text |
id | pubmed-10598582 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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