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MLGO: phylogeny reconstruction and ancestral inference from gene-order data
BACKGROUND: The rapid accumulation of whole-genome data has renewed interest in the study of using gene-order data for phylogenetic analyses and ancestral reconstruction. Current software and web servers typically do not support duplication and loss events along with rearrangements. RESULTS: MLGO (M...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4236499/ https://www.ncbi.nlm.nih.gov/pubmed/25376663 http://dx.doi.org/10.1186/s12859-014-0354-6 |
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author | Hu, Fei Lin, Yu Tang, Jijun |
author_facet | Hu, Fei Lin, Yu Tang, Jijun |
author_sort | Hu, Fei |
collection | PubMed |
description | BACKGROUND: The rapid accumulation of whole-genome data has renewed interest in the study of using gene-order data for phylogenetic analyses and ancestral reconstruction. Current software and web servers typically do not support duplication and loss events along with rearrangements. RESULTS: MLGO (Maximum Likelihood for Gene-Order Analysis) is a web tool for the reconstruction of phylogeny and/or ancestral genomes from gene-order data. MLGO is based on likelihood computation and shows advantages over existing methods in terms of accuracy, scalability and flexibility. CONCLUSIONS: To the best of our knowledge, it is the first web tool for analysis of large-scale genomic changes including not only rearrangements but also gene insertions, deletions and duplications. The web tool is available from http://www.geneorder.org/server.php. |
format | Online Article Text |
id | pubmed-4236499 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-42364992014-11-19 MLGO: phylogeny reconstruction and ancestral inference from gene-order data Hu, Fei Lin, Yu Tang, Jijun BMC Bioinformatics Software BACKGROUND: The rapid accumulation of whole-genome data has renewed interest in the study of using gene-order data for phylogenetic analyses and ancestral reconstruction. Current software and web servers typically do not support duplication and loss events along with rearrangements. RESULTS: MLGO (Maximum Likelihood for Gene-Order Analysis) is a web tool for the reconstruction of phylogeny and/or ancestral genomes from gene-order data. MLGO is based on likelihood computation and shows advantages over existing methods in terms of accuracy, scalability and flexibility. CONCLUSIONS: To the best of our knowledge, it is the first web tool for analysis of large-scale genomic changes including not only rearrangements but also gene insertions, deletions and duplications. The web tool is available from http://www.geneorder.org/server.php. BioMed Central 2014-11-08 /pmc/articles/PMC4236499/ /pubmed/25376663 http://dx.doi.org/10.1186/s12859-014-0354-6 Text en © Hu et al.; licensee BioMed Central Ltd. 2014 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. 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 Hu, Fei Lin, Yu Tang, Jijun MLGO: phylogeny reconstruction and ancestral inference from gene-order data |
title | MLGO: phylogeny reconstruction and ancestral inference from gene-order data |
title_full | MLGO: phylogeny reconstruction and ancestral inference from gene-order data |
title_fullStr | MLGO: phylogeny reconstruction and ancestral inference from gene-order data |
title_full_unstemmed | MLGO: phylogeny reconstruction and ancestral inference from gene-order data |
title_short | MLGO: phylogeny reconstruction and ancestral inference from gene-order data |
title_sort | mlgo: phylogeny reconstruction and ancestral inference from gene-order data |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4236499/ https://www.ncbi.nlm.nih.gov/pubmed/25376663 http://dx.doi.org/10.1186/s12859-014-0354-6 |
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