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ChromaClade: combined visualisation of phylogenetic and sequence data

BACKGROUND: Studying site-specific amino acid frequencies by eye can reveal biologically significant variability and lineage-specific adaptation. This so-called ‘sequence gazing’ often informs bioinformatics and experimental research. But it is important to also account for the underlying phylogeny,...

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Autores principales: Monit, Christopher, Goldstein, Richard A., Towers, Greg J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6792252/
https://www.ncbi.nlm.nih.gov/pubmed/31615393
http://dx.doi.org/10.1186/s12862-019-1518-9
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author Monit, Christopher
Goldstein, Richard A.
Towers, Greg J.
author_facet Monit, Christopher
Goldstein, Richard A.
Towers, Greg J.
author_sort Monit, Christopher
collection PubMed
description BACKGROUND: Studying site-specific amino acid frequencies by eye can reveal biologically significant variability and lineage-specific adaptation. This so-called ‘sequence gazing’ often informs bioinformatics and experimental research. But it is important to also account for the underlying phylogeny, since similarities may be due to common descent rather than selection pressure, and because it is important to distinguish between founder effects and convergent evolution. We set out to combine phylogenetic and sequence data to produce evolutionarily insightful visualisations. RESULTS: We present ChromaClade, a convenient tool with a graphical user-interface that works in concert with popular tree viewers to produce colour-annotated phylogenies highlighting residues found in each taxon and at each site in a sequence alignment. Colouring branches according to residues found at descendent tips also quickly identifies lineage-specific residues and those internal branches where key substitutions have occurred. We demonstrate applications of ChromaClade to human immunodeficiency virus and influenza A virus datasets, illustrating cases of conservative, adaptive and convergent evolution. CONCLUSIONS: We find this to be a powerful approach for visualising site-wise residue distributions and detecting evolutionary patterns, especially in large datasets. ChromaClade is available for Windows, macOS and Unix or Linux; program executables and source code are available at github.com/chrismonit/chroma_clade.
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spelling pubmed-67922522019-10-21 ChromaClade: combined visualisation of phylogenetic and sequence data Monit, Christopher Goldstein, Richard A. Towers, Greg J. BMC Evol Biol Software BACKGROUND: Studying site-specific amino acid frequencies by eye can reveal biologically significant variability and lineage-specific adaptation. This so-called ‘sequence gazing’ often informs bioinformatics and experimental research. But it is important to also account for the underlying phylogeny, since similarities may be due to common descent rather than selection pressure, and because it is important to distinguish between founder effects and convergent evolution. We set out to combine phylogenetic and sequence data to produce evolutionarily insightful visualisations. RESULTS: We present ChromaClade, a convenient tool with a graphical user-interface that works in concert with popular tree viewers to produce colour-annotated phylogenies highlighting residues found in each taxon and at each site in a sequence alignment. Colouring branches according to residues found at descendent tips also quickly identifies lineage-specific residues and those internal branches where key substitutions have occurred. We demonstrate applications of ChromaClade to human immunodeficiency virus and influenza A virus datasets, illustrating cases of conservative, adaptive and convergent evolution. CONCLUSIONS: We find this to be a powerful approach for visualising site-wise residue distributions and detecting evolutionary patterns, especially in large datasets. ChromaClade is available for Windows, macOS and Unix or Linux; program executables and source code are available at github.com/chrismonit/chroma_clade. BioMed Central 2019-10-15 /pmc/articles/PMC6792252/ /pubmed/31615393 http://dx.doi.org/10.1186/s12862-019-1518-9 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Monit, Christopher
Goldstein, Richard A.
Towers, Greg J.
ChromaClade: combined visualisation of phylogenetic and sequence data
title ChromaClade: combined visualisation of phylogenetic and sequence data
title_full ChromaClade: combined visualisation of phylogenetic and sequence data
title_fullStr ChromaClade: combined visualisation of phylogenetic and sequence data
title_full_unstemmed ChromaClade: combined visualisation of phylogenetic and sequence data
title_short ChromaClade: combined visualisation of phylogenetic and sequence data
title_sort chromaclade: combined visualisation of phylogenetic and sequence data
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6792252/
https://www.ncbi.nlm.nih.gov/pubmed/31615393
http://dx.doi.org/10.1186/s12862-019-1518-9
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