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ClustalW was one of the first multiple sequence alignment algorithms to combine pairwise alignment and global alignment to increase speed, but this decision reduces result accuracy. When multiple sequence alignment algorithms were compared in 2014, ClustalW was one of the fastest that was able to produce results at the desired level of accuracy.
First 90 positions of a protein multiple sequence alignment of instances of the acidic ribosomal protein P0 (L10E) from several organisms. Generated with ClustalX.. Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA.
In bioinformatics, MAFFT (multiple alignment using fast Fourier transform) is a program used to create multiple sequence alignments of amino acid or nucleotide sequences. . Published in 2002, the first version used an algorithm based on progressive alignment, in which the sequences were clustered with the help of the fast Fourier transfo
M-Coffee: a special mode of T-Coffee that makes it possible to combine the output of the most common multiple sequence alignment packages (Muscle, ClustalW, Mafft, ProbCons, etc.). The resulting alignments are slightly better than the individual one, but most importantly the program indicates the alignment regions where the various packages ...
S. Malikic, A.W. McPherson, N. Donmez, C.S. Sahinalp ClustalW Progressive multiple sequence alignment: Distance matrix/nearest neighbor: Thompson et al. [13] CoalEvol Simulation of DNA and protein evolution along phylogenetic trees (that can also be simulated with the coalescent) Simulation of multiple sequence alignments of DNA or protein ...
Quality control and filtering of multiple sequence alignments: Both: Local or global: O. Penn et al. 2010 (latest version 2015) Kalign Progressive alignment: Both: Global: T. Lassmann: 2005: MACSE Progressive-iterative alignment. Multiple alignment of coding sequences accounting for frameshifts and stop codons. Nucleotides Global V. Ranwez et al.
It is used widely by a variety of web servers (e.g. the EBI ClustalW server and the Pfam protein domain database) but is also available as a general purpose alignment editor. Jalview has a wide range of functions in addition to multiple sequence alignment generation, viewing and editing, including calculating phylogenetic trees and viewing ...
MacVector is a collection of sequence analysis algorithms linked to various sequence editors, including a single sequence editor, a multiple sequence alignment editor and a contig editor. MacVector tries to use a minimum of windows and steps to access all the functionality. Functions include: