Systematic exploration of guide-tree topology effects for small protein alignments

Author:

Sievers Fabian,Hughes Graham M,Higgins Desmond G

Publisher

Springer Science and Business Media LLC

Subject

Applied Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Structural Biology

Reference41 articles.

1. Needleman SB, Wunsch CD: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970, 48 (3): 443-453. 10.1016/0022-2836(70)90057-4. doi:10.1016/0022-2836(70)90057-4

2. Feng DF, Doolittle RF: Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol. 1987, 25 (4): 351-360. 10.1007/BF02603120.

3. Higgins DG, Bleasby AJ, Fuchs R: CLUSTAL V: improved software for multiple sequence alignment. Comput Appl Biosci. 1992, 8 (2): 189-191. doi:10.1093/bioinformatics/8.2.189

4. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG: Fast, scalable generation of high-quality protein multiple sequence alignments using clustal omega. Mol Syst Biol. 2011, 7 (539): doi:10.1038/msb.2011.75

5. Katoh K, Misawa K, Kuma K, Miyata T: Mafft: a novel method for rapid multiple sequence alignment based on fast fourier transform. Nucleic Acids Res. 2002, 30: 3059-3066. 10.1093/nar/gkf436.

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