ClustalW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice.
Thompson JD, Higgins DG, and Gibson TJ
Nucleic Acids Res. 1994 Nov 11;22(22):4673-80.
Clustal W and Clustal X version 2.0
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG
Bioinformatics. 2007 23:2947-2948
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Soding J, Thompson JD, Higgins DG
Molecular Systems Biology. 2011 7:539
MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Edgar RC
Nucleic Acids Res. 2004 32(5), 1792-97
T-Coffee: A novel method for fast and accurate multiple sequence alignment.
Notredame C, Higgins D, and Heringa J
Journal of Molecular Biology. 2000 302:205-217.
Recent developments in the MAFFT multiple sequence alignment program.
Katoh K, Toh H
Briefings in Bioinformatics. 2008 9(4):286-298
BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs.
Thompson JD, Plewniak F, Poch O.
Bioinformatics. 1999 Jan;15(1):87-8.
BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations.
Bahr A, Thompson JD, Thierry JC, Poch O.
Nucleic Acids Res. 2001 Jan 1;29(1):323-6.
Multiple sequence alignment modeling: methods and applications (updates on the latest changes in the field)
Chatzou M, Magis C, Chang JM, Kemena C, Bussotii G, Erb I, Notredame C
Briefings in Bioinformatics 2016 17(6):1009-1023
Recent evolutions of multiple sequence alignment algorithms. (written by the author of t-coffee)
Notredame C.
PLoS Comput Biol. 2007 Aug;3(8):e123.
Multiple sequence alignment. (written by the authors of muscle and probcons) Edgar RC, Batzoglou S. Curr Opin Struct Biol. 2006 Jun;16(3):368-73.
Analysis and comparison of benchmarks for multiple sequence alignment. (written by the author of Clustal and Coffee)
Blackshields G, Wallace IM, Larkin M, Higgins DG.
In Silico Biol. 2006;6(4):321-39.
Multiple sequence alignments.
Wallace IM, Blackshields G, Higgins DG. (written by the author of Clustal and Coffee)
Curr Opin Struct Biol. 2005 Jun;15(3):261-6.
Recent progress in multiple sequence alignment: a survey. (this written by the author of T-coffee, and before Muscle came out)
Notredame C.
Pharmacogenomics. 2002 Jan;3(1):131-44.
Benchmarking reviews:
Quality measures fro protein alignment benchmarks.
Edgar RC
Nucleic Acids Research. 2010 38:2145-53
Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment.
Iantorno S, Gori K, Goldman N, Gil M, Dessimoz C
Methods Mol Biol. 2014 1079:59-73
Other Programs Mentioned:
Global Multiple Alignment
Benchmarking
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