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:
\itemcpwThe basic function. Various command-line options are available, all of which are optional. If run with nothing on the command line, the program will assume you want to compare two alignments and print output to the screen, and will prompt for all other necessary information.
\itemread.nexusRead a nexus file and generate an object of class alignment.
\itemread.phylipRead a phylip file and generate an object of class alignment.
\itemaln.to.matrixTake the data from an alignment object and convert it into a taxa-by-characters matrix, with or without rownames.
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)