rdp_trainset9: RDP training set v9

In phylotypr: Classifying DNA Sequences to Taxonomic Groupings

RDP training set v9

Description

The sequence and taxonomy data for the 10,049 sequences found in the Ribosomal Database Project's trainset9_032012 training set for use with the naive Bayesian classifier as implemented in the {phylyotypr} R package. Originally released by the RDP in September 2012. The rdp version contains the same sequences as provided by the official RDP version (9,665 bacterial and 384 archaeal). The pds version contains extra eukaryotic sequences including 119 chloroplasts and mitochondria (10,168 total sequences). See the mothur reference file page in "Sources" for more information. Be sure to see the mothur GitHub project where you can find the phylotyprrefdata package (https://github.com/mothur/phylotyprrefdata) for access to other taxonomic reference data.

Usage

rdp_trainset9

rdp_trainset9_pds

Format

A classification_database object that holds two slots: seq_taxonomy_data and reference_data. The seq_taxonomy_data slot is a data.frame containing

sequence_name

Sequence accession identifier

sequence

DNA sequence string

taxonomy

Taxonomic string with each level separated with a ⁠;⁠

The reference_data slot contains metadata about the database and includes fields:

reference_vendor

Entity that created original database (e.g., RDP)

reference_versions

The version of database provided by original entity

reference_usages

For classification or alignment

reference_notes

Any additional notes about the database. Currently the version of phylotypr that provided the database

reference_urls

URLs where database can be obtained

reference_citation

Citation for database in BibTeX format

An object of class classification_database of length 2.

Source

• mothur-formatted files

• RDP sourceforge page # nolint: line_length_linter

phylotypr documentation built on Oct. 22, 2026, 5:21 p.m.