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...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2016-03-01
|
| Series: | Life |
| Subjects: | |
| Online Access: | http://www.mdpi.com/2075-1729/6/1/11 |
| _version_ | 1798040661458419712 |
|---|---|
| author | Fabian Klötzl Bernhard Haubold |
| author_facet | Fabian Klötzl Bernhard Haubold |
| author_sort | Fabian Klötzl |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-11T22:10:39Z |
| format | Article |
| id | doaj.art-5716e4c43a5f4be890c5b4375e3800de |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-04-11T22:10:39Z |
| publishDate | 2016-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-5716e4c43a5f4be890c5b4375e3800de2022-12-22T04:00:33ZengMDPI AGLife2075-17292016-03-01611110.3390/life6010011life6010011Support Values for Genome PhylogeniesFabian Klötzl0Bernhard Haubold1Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, GermanyDepartment of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, GermanyWe 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.http://www.mdpi.com/2075-1729/6/1/11bootstrapquartet analysissupport valuephylogenydistance matrix |
| spellingShingle | Fabian Klötzl Bernhard Haubold Support Values for Genome Phylogenies Life bootstrap quartet analysis support value phylogeny distance matrix |
| 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 | bootstrap quartet analysis support value phylogeny distance matrix |
| url | http://www.mdpi.com/2075-1729/6/1/11 |
| work_keys_str_mv | AT fabianklotzl supportvaluesforgenomephylogenies AT bernhardhaubold supportvaluesforgenomephylogenies |