PhyloTreePruner: A Phylogenetic Tree-Based Approach for selection of Orthologous sequences for phylogenomics
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...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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SAGE Publishing
2013-01-01
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| Series: | Evolutionary Bioinformatics |
| Online Access: | https://doi.org/10.4137/EBO.S12813 |
| _version_ | 1830302331641528320 |
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| author | Kevin M. Kocot Mathew R. Citarella Leonid L. Moroz Kenneth M. Halanych |
| author_facet | Kevin M. Kocot Mathew R. Citarella Leonid L. Moroz Kenneth M. Halanych |
| author_sort | Kevin M. Kocot |
| collection | DOAJ |
| description | 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 /. |
| first_indexed | 2024-12-19T09:05:00Z |
| format | Article |
| id | doaj.art-223e4293e8a54216b0ffd5d832654638 |
| institution | Directory Open Access Journal |
| issn | 1176-9343 |
| language | English |
| last_indexed | 2024-12-19T09:05:00Z |
| publishDate | 2013-01-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Evolutionary Bioinformatics |
| spelling | doaj.art-223e4293e8a54216b0ffd5d8326546382022-12-21T20:28:23ZengSAGE PublishingEvolutionary Bioinformatics1176-93432013-01-01910.4137/EBO.S12813PhyloTreePruner: A Phylogenetic Tree-Based Approach for selection of Orthologous sequences for phylogenomicsKevin M. Kocot0Mathew R. Citarella1Leonid L. Moroz2Kenneth M. Halanych3These authors contributed equally to this work.These authors contributed equally to this work.McKnight Brain Institute, University of Florida, Gainesville, Florida, USA.Department of Biological Sciences, 101 Rouse Life Sciences, Auburn University, Auburn, USA.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 /.https://doi.org/10.4137/EBO.S12813 |
| spellingShingle | Kevin M. Kocot Mathew R. Citarella Leonid L. Moroz Kenneth M. Halanych PhyloTreePruner: A Phylogenetic Tree-Based Approach for selection of Orthologous sequences for phylogenomics Evolutionary Bioinformatics |
| title | PhyloTreePruner: A Phylogenetic Tree-Based Approach for selection of Orthologous sequences for phylogenomics |
| title_full | PhyloTreePruner: A Phylogenetic Tree-Based Approach for selection of Orthologous sequences for phylogenomics |
| title_fullStr | PhyloTreePruner: A Phylogenetic Tree-Based Approach for selection of Orthologous sequences for phylogenomics |
| title_full_unstemmed | PhyloTreePruner: A Phylogenetic Tree-Based Approach for selection of Orthologous sequences for phylogenomics |
| title_short | PhyloTreePruner: A Phylogenetic Tree-Based Approach for selection of Orthologous sequences for phylogenomics |
| title_sort | phylotreepruner a phylogenetic tree based approach for selection of orthologous sequences for phylogenomics |
| url | https://doi.org/10.4137/EBO.S12813 |
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