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PentaPlot: A software tool for the illustration of genome mosaicism
BACKGROUND: Dekapentagonal maps depict the phylogenetic relationships of five genomes in a visually appealing diagram and can be viewed as an alternative to a single evolutionary consensus tree. In particular, the generated maps focus attention on those gene families that significantly deviate from...
Autores principales: | , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2005
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1177926/ https://www.ncbi.nlm.nih.gov/pubmed/15938752 http://dx.doi.org/10.1186/1471-2105-6-139 |
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author | Hamel, Lutz Zhaxybayeva, Olga Gogarten, J Peter |
author_facet | Hamel, Lutz Zhaxybayeva, Olga Gogarten, J Peter |
author_sort | Hamel, Lutz |
collection | PubMed |
description | BACKGROUND: Dekapentagonal maps depict the phylogenetic relationships of five genomes in a visually appealing diagram and can be viewed as an alternative to a single evolutionary consensus tree. In particular, the generated maps focus attention on those gene families that significantly deviate from the consensus or plurality phylogeny. PentaPlot is a software tool that computes such dekapentagonal maps given an appropriate probability support matrix. RESULTS: The visualization with dekapentagonal maps critically depends on the optimal layout of unrooted tree topologies representing different evolutionary relationships among five organisms along the vertices of the dekapentagon. This is a difficult optimization problem given the large number of possible layouts. At its core our tool utilizes a genetic algorithm with demes and a local search strategy to search for the optimal layout. The hybrid genetic algorithm performs satisfactorily even in those cases where the chosen genomes are so divergent that little phylogenetic information has survived in the individual gene families. CONCLUSION: PentaPlot is being made publicly available as an open source project at . |
format | Text |
id | pubmed-1177926 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2005 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-11779262005-07-21 PentaPlot: A software tool for the illustration of genome mosaicism Hamel, Lutz Zhaxybayeva, Olga Gogarten, J Peter BMC Bioinformatics Software BACKGROUND: Dekapentagonal maps depict the phylogenetic relationships of five genomes in a visually appealing diagram and can be viewed as an alternative to a single evolutionary consensus tree. In particular, the generated maps focus attention on those gene families that significantly deviate from the consensus or plurality phylogeny. PentaPlot is a software tool that computes such dekapentagonal maps given an appropriate probability support matrix. RESULTS: The visualization with dekapentagonal maps critically depends on the optimal layout of unrooted tree topologies representing different evolutionary relationships among five organisms along the vertices of the dekapentagon. This is a difficult optimization problem given the large number of possible layouts. At its core our tool utilizes a genetic algorithm with demes and a local search strategy to search for the optimal layout. The hybrid genetic algorithm performs satisfactorily even in those cases where the chosen genomes are so divergent that little phylogenetic information has survived in the individual gene families. CONCLUSION: PentaPlot is being made publicly available as an open source project at . BioMed Central 2005-06-06 /pmc/articles/PMC1177926/ /pubmed/15938752 http://dx.doi.org/10.1186/1471-2105-6-139 Text en Copyright © 2005 Hamel et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Software Hamel, Lutz Zhaxybayeva, Olga Gogarten, J Peter PentaPlot: A software tool for the illustration of genome mosaicism |
title | PentaPlot: A software tool for the illustration of genome mosaicism |
title_full | PentaPlot: A software tool for the illustration of genome mosaicism |
title_fullStr | PentaPlot: A software tool for the illustration of genome mosaicism |
title_full_unstemmed | PentaPlot: A software tool for the illustration of genome mosaicism |
title_short | PentaPlot: A software tool for the illustration of genome mosaicism |
title_sort | pentaplot: a software tool for the illustration of genome mosaicism |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1177926/ https://www.ncbi.nlm.nih.gov/pubmed/15938752 http://dx.doi.org/10.1186/1471-2105-6-139 |
work_keys_str_mv | AT hamellutz pentaplotasoftwaretoolfortheillustrationofgenomemosaicism AT zhaxybayevaolga pentaplotasoftwaretoolfortheillustrationofgenomemosaicism AT gogartenjpeter pentaplotasoftwaretoolfortheillustrationofgenomemosaicism |