期刊
EVOLUTIONARY BIOINFORMATICS
卷 9, 期 -, 页码 429-435出版社
SAGE PUBLICATIONS LTD
DOI: 10.4137/EBO.S12813
关键词
phylogenomic; orthology; paralogy; gene tree
资金
- NSF [DEB-1210518, DEB-1036537, IOS-0843473, IOS-1146575, CNS-0821622]
- McKnight Brain Research Foundation
- University of Florida
- NIH [5R01GM097502, R01MH097062, 5R21DA030118]
- NASA [11-EXO11-0127]
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM097502] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF MENTAL HEALTH [R01MH097062] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE ON DRUG ABUSE [R21DA030118] Funding Source: NIH RePORTER
- Direct For Biological Sciences [1146575] Funding Source: National Science Foundation
- Division Of Environmental Biology [1036537] Funding Source: National Science Foundation
Molecular phylogenetics relies on accurate identification of orthologous sequences among the taxa of interest. Most orthology inference programs available for use in phylogenomics rely on small sets of pre-defined orthologs from model organisms or phenetic approaches such as all-versus-all sequence comparisons followed by Markov graph-based clustering. Such approaches have high sensitivity but may erroneously include paralogous sequences. We developed PhyloTreePruner, a software utility that uses a phylogenetic approach to refine orthology inferences made using phenetic methods. PhyloTreePruner checks single-gene trees for evidence of paralogy and generates a new alignment for each group containing only sequences inferred to be orthologs. Importantly, PhyloTreePruner takes into account support values on the tree and avoids unnecessarily deleting sequences in cases where a weakly supported tree topology incorrectly indicates paralogy. A test of PhyloTreePruner on a dataset generated from 11 completely sequenced arthropod genomes identified 2,027 orthologous groups sampled for all taxa. Phylogenetic analysis of the concatenated supermatrix yielded a generally well-supported topology that was consistent with the current understanding of arthropod phylogeny. PhyloTreePruner is freely available from http://sourceforge.net/projects/phylotreepruner/.
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