3DCoffee: Combining Protein Sequences and Structures within Multiple Sequence Alignments

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

Julie Thompson, Desmond G. Higgins, Toby J. Gibson · Nucleic Acids Research · 1994 · 64.9K citations · Full text

Life Sciences, Bioinformatics, Sequence Analysis +14

The neighbor-joining method: a new method for reconstructing phylogenetic trees.

Naruya Saitou, M Nei · Molecular Biology and Evolution · 1987 · 60.5K citations · Full text

Life Sciences, Bioinformatics, Evolutionary Biology +17

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

Kazutaka Katoh · Nucleic Acids Research · 2002 · 17.8K citations · Full text

Life Sciences, Bioinformatics, Biology +13

A general method applicable to the search for similarities in the amino acid sequence of two proteins

Saul B. Needleman, Christian D. Wunsch · Journal of Molecular Biology · 1970 · 11.5K citations

Life Sciences, Biochemistry, Bioinformatics +13

Identification of common molecular subsequences

Temple F. Smith, Michael S. Waterman · Journal of Molecular Biology · 1981 · 10.1K citations

Life Sciences, Bioinformatics, Molecular Biology +11