Concepedia

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

Donovan H. Parks, Maria Chuvochina, David W. Waite, Christian Rinke, Adam Skarshewski, Pierre-Alain Chaumeil, Philip Hugenholtz

Nature Biotechnology · 2018 · 3.9K citations · 79 references

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79

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis · Bioinformatics · 2014 · 34.3K citations · Full text

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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

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BLAST+: architecture and applications

Christiam Camacho, George Coulouris, Vahram Avagyan et al. · BMC Bioinformatics · 2009 · 23.2K citations · Full text

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Prodigal: prokaryotic gene recognition and translation initiation site identification

Doug Hyatt, Gwo-Liang Chen, Philip LoCascio et al. · BMC Bioinformatics · 2010 · 13.1K citations · Full text

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CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Donovan H. Parks, Michael Imelfort, Connor T. Skennerton et al. · Genome Research · 2015 · 12.8K citations · Full text

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