phylotypr: an R package for classifying DNA sequences
Patrick D. Schloss
TL;DR
The phylotypr R package uses a Bayesian algorithm to classify DNA sequences into taxonomic groups, with supporting databases from major projects.
Contribution
A new R package and data companion for taxonomic classification of DNA sequences using Bayesian methods and curated databases.
Findings
phylotypr implements a naive Bayesian classifier for DNA sequences.
The phylotyprrefdata package provides multiple taxonomic databases from RDP, SILVA, and greengenes.
Abstract
The phylotypr R package implements the popular naive Bayesian classification algorithm that is frequently used to classify 16S rRNA and other gene sequences to taxonomic lineages. A companion data package, phylotyprrefdata, also provides numerous versions of taxonomic databases from the Ribosomal Database Project, SILVA, and greengenes.
Genes, proteins, chemicals, diseases, species, mutations and cell lines named across the full text — each resolved to its canonical identifier and authoritative record.
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Taxonomy
TopicsGenetic diversity and population structure · Genomics and Phylogenetic Studies · Genetic Mapping and Diversity in Plants and Animals