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Support Values for Genome Phylogenies
We have recently developed a distance metric for efficiently estimating the number of substitutions per site between unaligned genome sequences. These substitution rates are called “anchor distances” and can be used for phylogeny reconstruction. Most phylogenies come with bootstrap support values, w...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4810242/ https://www.ncbi.nlm.nih.gov/pubmed/26959064 http://dx.doi.org/10.3390/life6010011 |
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author | Klötzl, Fabian Haubold, Bernhard |
author_facet | Klötzl, Fabian Haubold, Bernhard |
author_sort | Klötzl, Fabian |
collection | PubMed |
description | We have recently developed a distance metric for efficiently estimating the number of substitutions per site between unaligned genome sequences. These substitution rates are called “anchor distances” and can be used for phylogeny reconstruction. Most phylogenies come with bootstrap support values, which are computed by resampling with replacement columns of homologous residues from the original alignment. Unfortunately, this method cannot be applied to anchor distances, as they are based on approximate pairwise local alignments rather than the full multiple sequence alignment necessary for the classical bootstrap. We explore two alternatives: pairwise bootstrap and quartet analysis, which we compare to classical bootstrap. With simulated sequences and 53 human primate mitochondrial genomes, pairwise bootstrap gives better results than quartet analysis. However, when applied to 29 E. coli genomes, quartet analysis comes closer to the classical bootstrap. |
format | Online Article Text |
id | pubmed-4810242 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-48102422016-04-04 Support Values for Genome Phylogenies Klötzl, Fabian Haubold, Bernhard Life (Basel) Article We have recently developed a distance metric for efficiently estimating the number of substitutions per site between unaligned genome sequences. These substitution rates are called “anchor distances” and can be used for phylogeny reconstruction. Most phylogenies come with bootstrap support values, which are computed by resampling with replacement columns of homologous residues from the original alignment. Unfortunately, this method cannot be applied to anchor distances, as they are based on approximate pairwise local alignments rather than the full multiple sequence alignment necessary for the classical bootstrap. We explore two alternatives: pairwise bootstrap and quartet analysis, which we compare to classical bootstrap. With simulated sequences and 53 human primate mitochondrial genomes, pairwise bootstrap gives better results than quartet analysis. However, when applied to 29 E. coli genomes, quartet analysis comes closer to the classical bootstrap. MDPI 2016-03-07 /pmc/articles/PMC4810242/ /pubmed/26959064 http://dx.doi.org/10.3390/life6010011 Text en © 2016 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons by Attribution (CC-BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Klötzl, Fabian Haubold, Bernhard Support Values for Genome Phylogenies |
title | Support Values for Genome Phylogenies |
title_full | Support Values for Genome Phylogenies |
title_fullStr | Support Values for Genome Phylogenies |
title_full_unstemmed | Support Values for Genome Phylogenies |
title_short | Support Values for Genome Phylogenies |
title_sort | support values for genome phylogenies |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4810242/ https://www.ncbi.nlm.nih.gov/pubmed/26959064 http://dx.doi.org/10.3390/life6010011 |
work_keys_str_mv | AT klotzlfabian supportvaluesforgenomephylogenies AT hauboldbernhard supportvaluesforgenomephylogenies |