TRAPID: an efficient online tool for the functional and comparative analysis of de novoRNA-Seq transcriptomes

Basic local alignment search tool

Stephen F. Altschul, Warren Gish, Webb Miller et al. · Journal of Molecular Biology · 1990 · 92.8K citations

Bioinformatics, Engineering, Information Retrieval +10

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

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

Stéphane Guindon, Jean-François Dufayard, Vincent Lefort et al. · Systematic Biology · 2010 · 18.4K citations · Full text

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

Morgan N. Price, Paramvir Dehal, Adam P. Arkin · PLoS ONE · 2010 · 15.1K citations · Full text

Jalview Version 2—a multiple sequence alignment editor and analysis workbench

Andrew Waterhouse, James B Procter, David Martin et al. · Bioinformatics · 2009 · 10.5K citations · Full text