Description Usage Arguments Details Author(s) References See Also Examples
View source: R/phrapl-utilities.R
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).
1 2 | RunSeqConverter(seqConvPath=system.file("extdata","seqConverter.pl",package="phrapl"),
inFilePath="./",inputFormat="nex")
|
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). |
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/
Brian O'Meara, Bryan Carstens, Nathan Jackson, Ariadna Morales-Garcia
Maintainer: Brian O'Meara <bomeara@utk.edu>
O'Meara, B.C., N. Jackson, A. Morales-Garcia, and B. Carstens (2014) Phrapl in prep.
RunRaxml
1 2 3 4 5 6 7 8 | ## 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)
|
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