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Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis

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Castresana, J.·2000·Molecular Biology and Evolution
DOI 10.1093/oxfordjournals.molbev.a026334
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Abstract

The use of some multiple-sequence alignments in phylogenetic analysis, particularly those that are not very well conserved, requires the elimination of poorly aligned positions and divergent regions, since they may not be homologous or may have been saturated by multiple substitutions. A computerized method that eliminates such positions and at the same time tries to minimize the loss of informative sites is presented here. The method is based on the selection of blocks of positions that fulfill a simple set of requirements with respect to the number of contiguous conserved positions, lack of gaps, and high conservation of flanking positions, making the final alignment more suitable for phylogenetic analysis. To illustrate the efficiency of this method, alignments of 10 mitochondrial proteins from several completely sequenced mitochondrial genomes belonging to diverse eukaryotes were used as examples. The percentages of removed positions were higher in the most divergent alignments. After removing divergent segments, the amino acid composition of the different sequences was more uniform, and pairwise distances became much smaller. Phylogenetic trees show that topologies can be different after removing conserved blocks, particularly when there are several poorly resolved nodes. Strong support was found for the grouping of animals and fungi but not for the position of more basal eukaryotes. The use of a computerized method such as the one presented here reduces to a certain extent the necessity of manually editing multiple alignments, makes the automation of phylogenetic analysis of large data sets feasible, and facilitates the reproduction of the final alignment by other researchers.

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Cited by

Metadata

Authors
Castresana, J.
Venue
Molecular Biology and Evolution
Publisher
Oxford University Press (OUP)
Published
2000-04-01
Volume
17
Issue
4
Pages
540-552
ISSN
  • 0737-4038 (ISSN-L)
  • 1537-1719
DOI
10.1093/oxfordjournals.molbev.a026334
OpenAlex
W1963957860
Cited by
10,508
References
2
FWCI
6.65
Type
journal article
Language
en
Open access
bronze

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