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High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
Article
Article
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
Chirag Jain; Luis M. Rodriguez‐R; Adam M. Phillippy; Konstantinos T. Konstantinidis; Srinivas Aluru · Nature Communications · 2018
A fundamental question in microbiology is whether there is continuum of genetic diversity among genomes, or clear species boundaries prevail instead. Whole-genome similarity metrics such as Average Nucleotide Identity (A...
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Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin
Article
Article
Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin
Nicholas A. Bokulich; Benjamin D. Kaehler; Jai Ram Rideout; Matthew R. Dillon; Evan Bolyen; Rob Knight; Gavin Huttley; J. Gregory Caporaso · Microbiome · 2018
BACKGROUND: Taxonomic classification of marker-gene sequences is an important step in microbiome analysis. RESULTS: We present q2-feature-classifier ( https://github.com/qiime2/q2-feature-classifier ), a QIIME 2 plugin c...
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MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms
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MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms
Sudhir Kumar; Glen Stecher; Michael Li; Christina Knyaz; Koichiro Tamura · Molecular Biology and Evolution · 2018
The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Micr...
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