Barking up the wrong treelength: The impact of gap penalty on alignment and tree accuracy

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 6, Issue 1, 2009, Pages 7-21

  Liu, Kevin ^a   Nelesen, Serita ^a   Raghavan, Sindhu ^a   Linder, C Randal ^b   Warnow, Tandy ^a  

^a University of Texas at Austin   (United States)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

Biology and genetics; Markov processes

Indexed keywords

ALIGNMENT METHODS; BIOLOGY AND GENETICS; GAP PENALTIES; MAXIMUM PARSIMONIES; NP-HARD; OPTIMIZATION PROBLEMS; PHYLOGENETIC TREES; POOR PERFORMANCE; SIMULATION STUDIES; SIMULTANEOUS ESTIMATIONS; TWO-PHASE METHODS;

BIOLOGY; CHROMOSOMES; MARKOV PROCESSES; OPTIMIZATION;

ALIGNMENT;

ARTICLE; BIOLOGICAL MODEL; BIOLOGY; COMPUTER PROGRAM; COMPUTER SIMULATION; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; PROBABILITY; SEQUENCE ALIGNMENT; STATISTICAL MODEL; SYSTEMS BIOLOGY;

COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; MARKOV CHAINS; MODELS, GENETIC; MODELS, STATISTICAL; PHYLOGENY; SEQUENCE ALIGNMENT; SOFTWARE; SYSTEMS BIOLOGY;

EID: 59649130312     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2008.63     Document Type: Article

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