Article Abstract

	Title:	Phylogenies scores for exhaustive searches and parsimony scores searches
	Author:	Hyrum D. Carroll, Perry G. Ridge, Mark J. Clement, Quinn O. Snell
	Address:	Computer Science Department, Brigham Young University, 3361 TMCB, Provo, Utah 84602, USA. ' University of Nebraska – Lincoln, Lincoln, Nebraska 68505, USA. ' Computer Science Department, Brigham Young University, 2208 TMCB, Provo, Utah 84602, USA. ' Computer Science Department, Brigham Young University, 2208 TMCB, Provo, Utah 84602, USA
	Journal:	International Journal of Bioinformatics Research and Applications 2007 - Vol. 3, No.4  pp. 493 - 503
	Abstract:	Fundamental to Multiple Sequence Alignment (MSA) algorithms is modelling insertions and deletions (gaps). The most prevalent model is to use Gap Open Penalties (GOP) and Gap Extension Penalties (GEP). While GOP and GEP are well understood conceptually, their effects on MSA and consequently on phylogeny scores are not as well understood. We use exhaustive phylogeny searching to explore the effects of varying the GOP and GEP for three nuclear ribosomal data sets. Particular attention is given to optimal maximum likelihood and parsimony phylogeny scores for various alignments of a range of GOP and GEP and their respective distribution of phylogeny scores.
	Keywords:	multiple sequence alignment; MSA; maximum likelihood; maximum parsimony; exhaustive search; gap penalties; gap open penalties; GOP; gap extension penalties; GEP; phylogeny scores; bioinformatics; nuclear ribosomal data.
	DOI:	10.1504/IJBRA.2007.015417
		Purchase this Paper         Comment on the Paper