boxshade: Boxshade: Shading Multiple Aligned Sequences

In mhahsler/rMSA: Interface for Popular Multiple Sequence Alignment Tools

Boxshade: Shading Multiple Aligned Sequences

Description

Executes boxshade on a multiple sequence alignment.

Usage

boxshade(x, file, dev="pdf", param="-thr=0.5 -cons -def",
    pdfCrop=TRUE)
boxshade_help()

Arguments

x	a multiple alignment as an object of class DNAMultipleAlignment, RNAMultipleAlignment or AAMultipleAlignment.
file	output file
dev	used output device. Available are: ps, eps, hpgl, rtf, crt, ansi, vt, ascii, fig, pict, html and pdf.
param	character string with the command line parameters for clustal (see output of boxshade_help()).
pdfCrop	crop the pdf file if it is smaller than a page. Use FALSE if you want the results on a page or the alignment covers multiple pages.

Details

For installation details see: https://github.com/mhahsler/rMSA/blob/master/INSTALL

Value

Only a file is created.

Author(s)

Michael Hahsler

References

Boxshade has been written by Kay Hofmann and Michael D. Baron

Examples

## Not run: 
rna <- readRNAStringSet(system.file("examples/RNA_example.fasta",
	package="rMSA"))
rna <- narrow(rna, start=1, end=50)

al <- clustal(rna)

boxshade(al, file="alignment.pdf", dev="pdf")

## End(Not run)

mhahsler/rMSA documentation built on May 24, 2024, 3:36 p.m.