CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

By Julie Dawn Thompson, Desmond G. Higgins, Toby J. Gibson. 1994

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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability (2013, background): “In Figure 4 C , a structure-informed MSA (described below), with the middle aspartic acid correctly aligned, is shown.”
ANTIFUNGAL COMPOUND PRODUCED BY THE CASSAVA ENDOPHYTE Bacillus pumilus MAIIIM4A (2009, background): “, v.66, n.5, p.650-657, September/October 2009 DE GRYZE, S.; SIX, J.; MERCKX, S. Quantifying water-stable soil aggregate turnover and its implication for soil organic matter dynamics in a model study.”
COMPARISON OF RNA EXPRESSION PROFILES BETWEEN THE TWO GENERATIONS OF PORPHYRA YEZOENSIS (RHODOPHYTA), BASED ON EXPRESSED SEQUENCE TAG FREQUENCY ANALYSIS (2003, methodology): “To detect this event in P. yezoensis , the CLUSTAL W program (Thompson et al. 1994) was applied to make a multiple sequence alignment within each of the 1013 groups that contained EST sequences from both generations.”
Regulation of carbon dioxide fixation in the chemoautotroph Xanthobacter flavus (2000, background): “In addition, a fourth region of CysB involved in ligand response and/or multimerization is also conserved in all CbbR proteins.”
Toward the phylogeny of the family Lacertidae - Why 4708 base pairs of mtDNA sequences cannot draw the picture (2000, background): “A few recent studies showed that phylogenetic construction is more fruitful at lower levels (e.g. Thorpe et al., 1994; Fu et al., 1997; Harris et al., 1998b).”
Analysing natural diversity of arbuscular mycorrhizal fungi in olive tree (Olea europaea L.) plantations and assessment of the effectiveness of native fungal isolates as inoculants for commercial cultivars of olive plantlets (2004, methodology): “Multiple sequence alignments of gene sequences were carried out using the programme CLUSTALW (version 1.5;Thompson et al., 1994).”
Field and Laboratory Methods for DNA Studies on Deep-sea Isopod Crustaceans (2014, methodology): “The widely applied alignment programs ClustalW (Thompson et al. 1994) and MAFFT (Katoh et al. 2002) were used and subsequently alignments were checked and corrected by hand where necessary.”
Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes (2007, methodology): “To test whether observed differences in performance (FN = 30%, FP = 8% for RBH; vs FN = 44%, FP = 3% for RSD) might be attributable to the alternative methods used for alignment (local BLAST [25] vs global ClustalW [33]), RBH and RSD analyses are simulated using identical Pfam alignments (see Method”