ArticleEvolutionary bioinformatics online2013
PhyloTreePruner: A Phylogenetic Tree-Based Approach for Selection of Orthologous Sequences for Phylogenomics.
Article in Evolutionary bioinformatics online, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed.
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- Transcriptome data for an ancient 'living-fossil' mollusc, Entemnotrochus rumphii.Scientific data · 2024Article
- Selection and Gene Duplication Associated With High-Elevation Diversification in Pristimantis, the Largest Terrestrial Vertebrate Genus.Genome biology and evolution · 2024Article
- Incongruence in the phylogenomics era.Nature reviews. Genetics · 2023Review
- Venomous Noodles: The Evolution of Toxins in Nemertea through Positive Selection and Gene Duplication.Toxins · 2023Article
- Signatures of Extreme Longevity: A Perspective from Bivalve Molecular Evolution.Genome biology and evolution · 2023Article
- Scaphopoda is the sister taxon to Bivalvia: Evidence of ancient incomplete lineage sorting.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Potential Contribution of Ancient Introgression to the Evolution of a Derived Reproductive Strategy in Ricefishes.Genome biology and evolution · 2023Article
- Identifying and addressing methodological incongruence in phylogenomics: A review.Evolutionary applications · 2023Review
- Positive and Relaxed Selective Pressures Have Both Strongly Influenced the Evolution of Cryonotothenioid Fishes during Their Radiation in the Freezing Southern Ocean.Genome biology and evolution · 2023Article
- Synteny Identifies Reliable Orthologs for Phylogenomics and Comparative Genomics of the Brassicaceae.Genome biology and evolution · 2023Article
- A phylogenomic approach to resolving interrelationships of polyclad flatworms, with implications for life-history evolution.Royal Society open science · 2023Article
- Available data do not rule out Ctenophora as the sister group to all other Metazoa.Nature communications · 2023Article
- OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees.PLoS biology · 2022Article
- A Practical Guide to Design and Assess a Phylogenomic Study.Genome biology and evolution · 2022Article
- DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition.Systematic biology · 2022Article
- Comprehensive Species Sampling and Sophisticated Algorithmic Approaches Refute the Monophyly of Arachnida.Molecular biology and evolution · 2022Article
- Quantitative Insights into the Contribution of Nematocysts to the Adaptive Success of Cnidarians Based on Proteomic Analysis.Biology · 2022Article
6 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
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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