Document Detail

Alignment and topological accuracy of the direct optimization approach via POY and traditional phylogenetics via ClustalW + PAUP*.
MedLine Citation:
PMID:  17454974     Owner:  NLM     Status:  MEDLINE    
Direct optimization frameworks for simultaneously estimating alignments and phylogenies have recently been developed. One such method, implemented in the program POY, is becoming more common for analyses of variable length sequences (e.g., analyses using ribosomal genes) and for combined evidence analyses (morphology + multiple genes). Simulation of sequences containing insertion and deletion events was performed in order to directly compare a widely used method of multiple sequence alignment (ClustalW) and subsequent parsimony analysis in PAUP* with direct optimization via POY. Data sets were simulated for pectinate, balanced, and random tree shapes under different conditions (clocklike, non-clocklike, and ultrametric). Alignment accuracy scores for the implied alignments from POY and the multiple sequence alignments from ClustalW were calculated and compared. In almost all cases (99.95%), ClustalW produced more accurate alignments than POY-implied alignments, judged by the proportion of correctly identified homologous sites. Topological accuracy (distance to the true tree) for POY topologies and topologies generated under parsimony in PAUP* from the ClustalW alignments were also compared. In 44.94% of the cases, Clustal alignment tree reconstructions via PAUP* were more accurate than POY, whereas in 16.71% of the cases POY reconstructions were more topologically accurate (38.38% of the time they were equally accurate). Comparisons between POY hypothesized alignments and the true alignments indicated that, on average, as alignment error increased, topological accuracy decreased.
T Heath Ogden; Michael S Rosenberg
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Publication Detail:
Type:  Comparative Study; Evaluation Studies; Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Systematic biology     Volume:  56     ISSN:  1063-5157     ISO Abbreviation:  Syst. Biol.     Publication Date:  2007 Apr 
Date Detail:
Created Date:  2007-04-24     Completed Date:  2007-07-12     Revised Date:  2009-04-16    
Medline Journal Info:
Nlm Unique ID:  9302532     Medline TA:  Syst Biol     Country:  England    
Other Details:
Languages:  eng     Pagination:  182-93     Citation Subset:  IM    
Department of Biological Sciences, Idaho State University, Idaho 83209, USA.
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MeSH Terms
Cluster Analysis
Computer Simulation*
Models, Genetic
Sequence Alignment / methods*
Sequence Analysis, DNA*
Grant Support
Comment In:
Syst Biol. 2008 Aug;57(4):653-7   [PMID:  18709601 ]

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