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)