[39] Unified approach to alignment and phylogenies
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Up-regulation of neutrophil activating protein in Helicobacter pylori under high-salt stress: Structural and phylogenetic comparison with bacterial iron-binding ferritins
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
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