PyEvolve: a toolkit for statistical modelling of molecular evolution

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 · 64.4K citations · Full text

Evolutionary trees from DNA sequences: A maximum likelihood approach

Joseph Felsenstein · Journal of Molecular Evolution · 1981 · 14.7K citations

Phylogenetics, Molecular Ecology, Medicine +9

Nineteen Dubious Ways to Compute the Exponential of a Matrix, Twenty-Five Years Later

C Moler, Charles Van Loan · SIAM Review · 2003 · 2.3K citations

Numerical Analysis, Spectral Theory, Engineering +12

A codon-based model of nucleotide substitution for protein-coding DNA sequences.

Nick Goldman, Zefeng Yang · Molecular Biology and Evolution · 1994 · 2K citations

Genetics, Molecular Biology, Molecular Genetics +21

Global optimization of statistical functions with simulated annealing

William L. Goffe, Gary D. Ferrier, J.D. Rogers · Journal of Econometrics · 1994 · 1.6K citations

Large-scale Global Optimization, Approximation Theory, Simulation Optimization +1