rrna: rrna

In giraola/taxxo: Integrating and automatising tools for prokaryotes taxonogenomics

Description

Outputs a individual rRNA gene sequences and a multiple sequence alignment.

Usage

rrna(path, pattern, outdir = "rrna_out", subunit = "16S",
  kingdom = "bacteria", align = TRUE)

Arguments

path	is the full path to where genomes in fasta format are placed.
pattern	a pattern (like '.fasta') for recognizing the genome files.
outdir	a name for the output directory that will be created for results.
subunit	takes '16S' (default), '23S' or 'both'.
kingdom	takes 'bacteria' (default) or 'archaea'.
align	takes a logical (default, TRUE) indicating if sequence alignment is performed.

Examples

rrna(path='.',pattern='.fasta',outdir='rrna_output',subunit='16S',kingdom='bacteria')

giraola/taxxo documentation built on May 17, 2019, 5:25 a.m.