A weighting system and algorithm for aligning many phylogenetically related sequences

By O. Gotoh. 1995

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Citations in the corpus

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability (2013, background): “D i st a n c e i s e st i m a t e d b a s e d o n D P .”
Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework (2008, background): “function of G-INS-i has the Weighted sum-of-pairs (WSP [38]) term and the consistency [39] term that is derived from the pairwise alignments.”
MUSCLE: a multiple sequence alignment method with reduced time and space complexity (2004, methodology): “MUSCLE implements the following sequence weighting schemes: none (all sequences have equal weight), Henikoff [26], PSI-BLAST [27] (a variant of Henikoff), CLUSTALW's, GSC [28], and the three-way method [ 29 ].”
AL2CO: calculation of positional conservation in a protein sequence alignment (2001, methodology): “A wide variety of different methods have been proposed to calculate weights w k (Altschul et al., 1989; Sander and Schneider, 1991; Gerstein et al., 1994; Henikoff and Henikoff, 1994; Thompson et al., 1994b; Eddy et al., 1995; Gotoh, 1995; Krogh and Mitchison, 1995).”
The accuracy of several multiple sequence alignment programs for proteins (2006, methodology): “The last phase is the iterative refinement which optimizes the Gotoh's weighted sum of pairs (WSP) [26] score, with a group-to-group alignment [27] and the tree-dependent restriction partition technique [24].”
Recent developments in the MAFFT multiple sequence alignment program (2008, methodology): “Due to the increasing necessity for MSA of distant homologs, in 2005, we sought to improve the accuracy of MAFFT, and released Version 5 [14], which adopted a new objective function, the summation of a traditional weighted sum-of-pairs (WSP) score [24], and a consistency score similar to COFFEE [25]”
Multiple sequence alignment. (2006, unknown): “MAFFT and MUSCLE have a similar design, building on work done by Gotoh in the 1990s that culminated in the PRRN and PRRP programs [20,21], which achieved the best accuracy of their time but were relatively slow and were not widely adopted.”