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A Method of Alignment Masking for Refining the Phylogenetic Signal of Multiple Sequence Alignments.
MedLine Citation:
PMID:  23193120     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
Inaccurate inference of positional homologies in multiple sequence alignments and systematic errors introduced by alignment heuristics obfuscate phylogenetic inference. Alignment masking, the elimination of phylogenetically uninformative or misleading sites from an alignment before phylogenetic analysis is a common practice in phylogenetic analysis.While masking is often done manually, automated methods are necessary in order to handle the much larger datasets being prepared today. In this study we introduce the concept of subsplits and demonstrate their use in extracting phylogenetic signal from alignments. We design a clustering approach for alignment masking where each cluster contains similar columns-similarity being defined on the basis of compatible subsplits; our approach then identifies noisy clusters and eliminates them. Trees inferred from the columns in the retained clusters are found to be topologically closer to the reference trees. We test our method on numerous standard benchmarks (both synthetic and biological datasets) and compare its performance with other methods of alignment masking. We find that our method can eliminate sites more accurately than other methods, particularly on divergent data, and can improve the topologies of the inferred trees in likelihood based analyses. Software availability: upon request from the author.
Authors:
Vaibhav Rajan
Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-11-27
Journal Detail:
Title:  Molecular biology and evolution     Volume:  -     ISSN:  1537-1719     ISO Abbreviation:  Mol. Biol. Evol.     Publication Date:  2012 Nov 
Date Detail:
Created Date:  2012-11-29     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  8501455     Medline TA:  Mol Biol Evol     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Affiliation:
Research Scientist, Xerox Research Centre India, Bangalore, India.
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