prog.examl.getbootstrapseq: Program to generate a booststrap alignment

In olli0601/big.phylo: big.phylo

Description

Input parameters are 'indir', 'infile', 'outdir', 'bootstrap', 'by', 'resume' and 'verbose', and specified via an argv string, see the Examples. The 'bootstrap' option specifies the boostrap iteration number, e. g. '-bootstrap=0' for the first bootstrap iteration. The 'by' option specifies the way the boostrap alignment is created. Valid options are codon and nucleotide.

Usage

prog.examl.getbootstrapseq()

Value

NULL. A boostrap alignment is written to file in phylip format.

See Also

pipeline.ExaML.bootstrap.per.proc

Examples

require(big.phylo)
data(nz_h3n2)
#	H3N2 data is stored in 'seq' DNAbin matrix object
print( seq )							
#	write sequences to directory for processing
indir		<- getwd()
infile		<- 'nz_h3n2.R'
insignat	<- ''
save(seq, file=paste(indir, infile, sep='/'))	
#	create the command string
bs.id		<- 1
infile		<- substr(infile, 1, nchar(infile)-2)
argv		<<- cmd.examl.bsalignment(indir, infile, bs.id) 
argv		<<- unlist(strsplit(argv,' '))
#	create the bootstrap alignment
prog.examl.getbootstrapseq()

olli0601/big.phylo documentation built on Nov. 9, 2019, 9:25 a.m.