The Hedgehog gene family of the cnidarian, Nematostella vectensis, and implications for understanding metazoan Hedgehog pathway evolution

MUSCLE: multiple sequence alignment with high accuracy and high throughput

R. C. Edgar · Nucleic Acids Research · 2004 · 45.3K citations · Full text

Genetics, Molecular Biology, Genomics +17

MrBayes 3: Bayesian phylogenetic inference under mixed models

Fredrik Ronquist, John P. Huelsenbeck · Bioinformatics · 2003 · 29.1K citations · Full text

Biology, Phylogenetics, Molecular Ecology +14

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

Stéphane Guindon, Olivier Gascuel · Systematic Biology · 2003 · 16.8K citations · Full text

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

Alexandros Stamatakis · Bioinformatics · 2006 · 15.7K citations · Full text

ProtTest: selection of best-fit models of protein evolution

Federico Abascal, Rafael Zardoya, David Posada · Computer applications in the biosciences · 2005 · 3.1K citations · Full text