Chloroplast genomes of two Mediterranean Bupleurum species and the phylogenetic relationship inferred from combined analysis with East Asian species

Fast gapped-read alignment with Bowtie 2

Ben Langmead, Steven L. Salzberg · Nature Methods · 2012 · 61.1K citations

Life Sciences, Bioinformatics, Molecular Biology +11

MrBayes 3: Bayesian phylogenetic inference under mixed models

Fredrik Ronquist, John P. Huelsenbeck · Bioinformatics · 2003 · 29.4K citations · Full text

Life Sciences, Bioinformatics, Evolutionary Biology +17

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen, Heiko A. Schmidt, Arndt von Haeseler et al. · Molecular Biology and Evolution · 2014 · 27.5K citations · Full text

Life Sciences, Bioinformatics, Biology +15

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Anton Bankevich, Sergey Nurk, Dmitry Antipov et al. · Journal of Computational Biology · 2012 · 27.2K citations

Life Sciences, Bioinformatics, Microbiology +17

ModelFinder: fast model selection for accurate phylogenetic estimates

Subha Kalyaanamoorthy, Bùi Quang Minh, Thomas K. F. Wong et al. · Nature Methods · 2017 · 18.8K citations

Life Sciences, Bioinformatics, Evolutionary Biology +13