PhyloTreePruner: A Phylogenetic Tree-Based Approach for selection of Orthologous sequences for phylogenomics
Year: 2013
Type: article
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/.
Source: Evolutionary Bioinformatics
DOI: 10.4137/ebo.s12813
Institutions: Auburn University, University of Florida
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,650
Funders: National Science Foundation, National Aeronautics and Space Administration, Brain Research Foundation, McKnight Foundation, Evelyn F. McKnight Brain Research Foundation, Auburn University, National Institutes of Health, National Institute of Mental Health, National Institute on Drug Abuse, National Institute of General Medical Sciences, Division of Integrative Organismal Systems, Division of Environmental Biology
Awards: MRI: Acquisition of Instrumentation for Coupled Experimental-Computational Neuroscience and Biology Research, Identifying mechanisms of symbiosis: Establishment and comparative physiology of siboglinid tubeworm/ bacterial interactions, G2956308198, Spatial Organization of the Genome in Identified Neurons of Memory Circuits, Signal Molecules in Ctenophores: Quest for the earliest neurotransmitters, Genomic Approaches to Deciphering Memory Circuits, Genomic Bases of Behavioral Learning: Single Cell Approaches, G636524684, Collaborative Research: WormNet II: Assembling the Annelid Tree of Life, DISSERTATION RESEARCH: Assessing early molluscan evolution with emphasis on aplacophorans
OpenAlex ID: W2038740993