mothur: mothur nucleotide

In mutolisp/seqParser: Parsing DNA sequences (seqParser)

Description

mothur nucleotide

Usage

mothur(binPath, subfunc, ...)

Arguments

binPath	mothur binary directory
subfunc	query sequences

Examples

## Not run: 
mothurDir <- '~/Downloads/mothur/'
fastaFile <-  './1060501B_cut3_without_N.fas'

phylipFile <-  paste(strsplit(fastaFile, '.fas')[1], '.phylip.dist', sep='')
listFile <- paste(strsplit(fastaFile, '.fas')[1], '.phylip.fn.list', sep='')

mothur(mothurDir, subfunc='dist.seqs',
       fasta=fastaFile, calc='onegap', cutoff=0.03, countends=F, output='lt')
mothur(mothurDir, subfunc='cluster',
       phylip=phylipFile,
       method='furthest',cutoff=0.03)
mothur(mothurDir, subfunc='bin.seqs',
       list=listFile, fasta=fastaFile)

## End(Not run)

mutolisp/seqParser documentation built on May 23, 2019, 10:52 a.m.