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  Support values for genome phylogenies

Klötzl, F., & Haubold, B. (2016). Support values for genome phylogenies. Life, 6(1): 11. doi:10.3390/life6010011.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-002A-056F-1 Version Permalink: http://hdl.handle.net/21.11116/0000-0005-1A9B-0
Genre: Journal Article

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Kloetzl_Haubold_2016.pdf (Publisher version), 601KB
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http://www.mdpi.com/2075-1729/6/1/11 (Publisher version)
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 Creators:
Klötzl, Fabian1, Author              
Haubold, Bernhard1, Author              
Affiliations:
1Research Group Bioinformatics, Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445644              

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Free keywords: bootstrap; quartet analysis; support value; phylogeny; distance matrix
 Abstract: 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.

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Language(s): eng - English
 Dates: 2016-02-032015-12-072016-02-232016-03-072016
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
 Rev. Method: Peer
 Identifiers: DOI: 10.3390/life6010011
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Title: Life
Source Genre: Journal
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Publ. Info: Basel, Switzerland : MDPI AG
Pages: - Volume / Issue: 6 (1) Sequence Number: 11 Start / End Page: - Identifier: Other: 2075-1729
CoNE: https://pure.mpg.de/cone/journals/resource/2075-1729