RunSeqConverter: Run SeqConverter to convert across sequence formats

In bomeara/phrapl: Phylogeography using Approximate Likelihood

Description

This function runs a perl script that takes one or more sequence files in nexus, fasta, or Se-Al formats and converts them to (relax) phylip format. This format is required for RAxML (RunRaxml).

Usage

RunSeqConverter(seqConvPath=system.file("extdata","seqConverter.pl",package="phrapl"),
	inFilePath="./",inputFormat="nex")

Arguments

seqConvPath	Path to the seqConverter script (default is to the script distributed with phrapl).
inFilePath	Path to the sequence files (default is current dir).
inputFormat	Format of sequence files. Default input format is "nex", but can also be "fasta" or "seal" (Se-Al). The sequence files must end with one of these suffixes (e.g. *.fas, *.nex, *.seal).

Details

The script "seqConverter.pl" can be found in "/home_path/phrapl/pkg/extdata/"

This perl script was written by Olaf R.P. Bininda-Emonds. For more information see: http://www.uni-oldenburg.de/ibu/systematik-evolutionsbiologie/programme/

Author(s)

Brian O'Meara, Bryan Carstens, Nathan Jackson, Ariadna Morales-Garcia

Maintainer: Brian O'Meara <[e-mail]>

References

O'Meara, B.C., N. Jackson, A. Morales-Garcia, and B. Carstens (2014) Phrapl in prep.

See Also

RunRaxml

Examples

## Not run: 
## The script "seqConverter.pl" can be found in "/home_path/phrapl/pkg/extdata/"
inFilePath<-load("/path/sequence_files")

RunSeqConverter(seqConvPath="/phrapl/pkg/extdata/seqConverter.pl", 
inFilePath=inFilePath, inputFormat="nex")

## End(Not run)

bomeara/phrapl documentation built on Feb. 8, 2021, 6:45 p.m.