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

Description Usage Arguments Examples

Identifies and extracts a set of 37 archaeal universal proteins used as phylogenetic markers.

Identifies and extracts a desired gene used as taxonomic/phylogenetic marker.

aprot(pattern = ".faa", path = ".", outdir = "mgene_output", marker,
  proc = 2)

aprot(pattern = ".faa", path = ".", outdir = "mgene_output", marker,
  proc = 2)

`pattern`	a pattern (like '.faa') for recognizing the annotation files.
`path`	is the full path to where genome annotations in fasta format are placed.
`outdir`	a name for the output directory that will be created for results.
`marker`	is the multifasta file in amino acids for the desired marker gene.
`proc`	is the number of threads used for protein searches.
`path`	is the full path to where genome annotations in fasta format are placed.
`pattern`	is a pattern (like '.faa') for recognizing the annotation files.
`outdir`	is a name for the output directory that will be created for results.
`proc`	is the number of threads used for protein searches.

1 2	aprot(path='./prodigal_output',pattern='.faa',outdir='aprot_output',proc=2) mgene(path='./prodigal_output',pattern='.faa',marker='gyrB.faa',outdir='mgene_output',proc=2)