[39] Unified approach to alignment and phylogenies
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2013, BiochimieCitation Excerpt :The alignment, phylogenetic analysis, and estimation of sequence divergence were carried out by using MEGALIGN and PROTEAN programs (DNASTAR, Madison, WI). A phylogenetic tree was constructed based on the percent divergence between protein sequences using a combination of distance matrix and approximate parsimony methods in the phylogeny generation program of Hein [36]. The tree was built using the CLUSTAL V program and weighted residue-weight table.
Alignment of, and phylogenetic inference from, random sequences: The susceptibility of alternative alignment methods to creating artifactual resolution and support
2010, Molecular Phylogenetics and EvolutionCitation Excerpt :This approach has variously been described as using a “hodgepodge of criteria” (Ogden and Whiting, 2003, p. 441), being used “mainly due to tradition” (Giribet, 2005, p. 396), “inappropriate for the reconstruction of phylogeny” (Mindell, 1991a, p. 78), or even being “fundamentally flawed” (Lunter et al., 2005, p. 2). Furthermore, it has been asserted that simultaneous alignment assumes a “star” phylogeny wherein all sequences are equally related to one another (Hein, 1990; Mindell, 1991a). In contrast, we suggest that simultaneous alignment using the similarity criterion followed by tree search simply avoids biasing the results in favor of any particular tree topology.
Approximation algorithms for constrained generalized tree alignment problem
2009, Discrete Applied MathematicsCitation Excerpt :Wang and Gusfield [14,17,18] presented an improved version of 2-approximation algorithm and the polynomial-time approximation scheme. From the perspective of heuristics, Sankoff [12], Kruskal and Sankoff [11] and Altschul and Lipman [1], proposed iterative methods for tree alignment, Hein [7,8] introduced an approach for tree alignment based on the concept of sequence graph. For an excellent overview of algorithms for tree alignment and related problems, we refer the reader to Gusfield [6], and Wang and Jiang [16].
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