| ComPairWise-package {ComPairWise} | R Documentation |
ComPairWise compares alternate alignments of a single DNA/RNA data set, and determines which columns are identically aligned. It also contains functions for reading NEXUS and PHYLIP-format alignment files.
| Package: | ComPairWise |
| Type: | Package |
| Version: | 1.01 |
| Date: | 2007-10-07 |
| License: | GNU GPL 2.0 or greater |
Contents:
The package also includes code to read NEXUS and PHYLIP alignments, which can be used as stand-alone functions.
Trina E. Roberts
Maintainer: Trina E. Roberts <trina.roberts@uaf.edu>
Roberts, T.E. and L.E. Olson. ComPairWise...
#The simplest case: 2 alignments, no options changed:
## Not run:
oldwd <- getwd()
setwd(file.path(.Library, "ComPairWise", "examples"))
cpw("sample.nex", "sample2.nex")
setwd(oldwd)
rm(oldwd)
## End(Not run)
#other functions
## Not run:
oldwd <- getwd()
setwd(file.path(.Library, "ComPairWise", "examples"))
nex.aln <- read.nexus("sample.nex")
setwd(oldwd)
rm(oldwd)
## End(Not run)
## Not run:
oldwd <- getwd()
setwd(file.path(.Library, "ComPairWise", "examples"))
phy.aln <- read.phylip("sample.phy")
setwd(oldwd)
rm(oldwd)
## End(Not run)
data(sample.aln)
aln1.mat <- aln.to.matrix(sample.aln)