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EvoFreq: visualization of the Evolutionary Frequencies of sequence and model data

BACKGROUND: High throughput sequence data has provided in depth means of molecular characterization of populations. When recorded at numerous time steps, such data can reveal the evolutionary dynamics of the population under study by tracking the changes in genotype frequencies over time. This neces...

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Detalles Bibliográficos
Autores principales: Gatenbee, Chandler D., Schenck, Ryan O., Bravo, Rafael R., Anderson, Alexander R. A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6916070/
https://www.ncbi.nlm.nih.gov/pubmed/31842729
http://dx.doi.org/10.1186/s12859-019-3173-y
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author Gatenbee, Chandler D.
Schenck, Ryan O.
Bravo, Rafael R.
Anderson, Alexander R. A.
author_facet Gatenbee, Chandler D.
Schenck, Ryan O.
Bravo, Rafael R.
Anderson, Alexander R. A.
author_sort Gatenbee, Chandler D.
collection PubMed
description BACKGROUND: High throughput sequence data has provided in depth means of molecular characterization of populations. When recorded at numerous time steps, such data can reveal the evolutionary dynamics of the population under study by tracking the changes in genotype frequencies over time. This necessitates a simple and flexible means of visualizing an increasingly complex set of data. RESULTS: Here we offer EvoFreq as a comprehensive tool set to visualize the evolutionary and population frequency dynamics of clones at a single point in time or as population frequencies over time using a variety of informative methods. EvoFreq expands substantially on previous means of visualizing the clonal, temporal dynamics and offers users a range of options for displaying their sequence or model data. CONCLUSIONS: EvoFreq, implemented in R with robust user options and few dependencies, offers a high-throughput means of quickly building, and interrogating the temporal dynamics of hereditary information across many systems. EvoFreq is freely available via https://github.com/MathOnco/EvoFreq.
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spelling pubmed-69160702019-12-30 EvoFreq: visualization of the Evolutionary Frequencies of sequence and model data Gatenbee, Chandler D. Schenck, Ryan O. Bravo, Rafael R. Anderson, Alexander R. A. BMC Bioinformatics Software BACKGROUND: High throughput sequence data has provided in depth means of molecular characterization of populations. When recorded at numerous time steps, such data can reveal the evolutionary dynamics of the population under study by tracking the changes in genotype frequencies over time. This necessitates a simple and flexible means of visualizing an increasingly complex set of data. RESULTS: Here we offer EvoFreq as a comprehensive tool set to visualize the evolutionary and population frequency dynamics of clones at a single point in time or as population frequencies over time using a variety of informative methods. EvoFreq expands substantially on previous means of visualizing the clonal, temporal dynamics and offers users a range of options for displaying their sequence or model data. CONCLUSIONS: EvoFreq, implemented in R with robust user options and few dependencies, offers a high-throughput means of quickly building, and interrogating the temporal dynamics of hereditary information across many systems. EvoFreq is freely available via https://github.com/MathOnco/EvoFreq. BioMed Central 2019-12-16 /pmc/articles/PMC6916070/ /pubmed/31842729 http://dx.doi.org/10.1186/s12859-019-3173-y Text en © The Author(s) 2019 Open Access This 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
Gatenbee, Chandler D.
Schenck, Ryan O.
Bravo, Rafael R.
Anderson, Alexander R. A.
EvoFreq: visualization of the Evolutionary Frequencies of sequence and model data
title EvoFreq: visualization of the Evolutionary Frequencies of sequence and model data
title_full EvoFreq: visualization of the Evolutionary Frequencies of sequence and model data
title_fullStr EvoFreq: visualization of the Evolutionary Frequencies of sequence and model data
title_full_unstemmed EvoFreq: visualization of the Evolutionary Frequencies of sequence and model data
title_short EvoFreq: visualization of the Evolutionary Frequencies of sequence and model data
title_sort evofreq: visualization of the evolutionary frequencies of sequence and model data
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6916070/
https://www.ncbi.nlm.nih.gov/pubmed/31842729
http://dx.doi.org/10.1186/s12859-019-3173-y
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