ComPairWise-package       package:ComPairWise       R Documentation

_C_o_m_p_a_r_e _p_h_y_l_o_g_e_n_e_t_i_c _o_r _p_o_p_u_l_a_t_i_o_n _g_e_n_e_t_i_c _D_N_A/_R_N_A _a_l_i_g_n_m_e_n_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     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.

_D_e_t_a_i_l_s:


       Package:  ComPairWise
       Type:     Package
       Version:  1.01
       Date:     2007-10-07
       License:  GNU GPL 2.0 or greater

     Contents:

_c_p_w The 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.  

_r_e_a_d._n_e_x_u_s Read a nexus file and generate an object of class alignment.

_r_e_a_d._p_h_y_l_i_p Read a phylip file and generate an object of class
     alignment.

_a_l_n._t_o._m_a_t_r_i_x Take 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.

_A_u_t_h_o_r(_s):

     Trina E. Roberts

     Maintainer: Trina E. Roberts <trina.roberts@uaf.edu>

_R_e_f_e_r_e_n_c_e_s:

     Roberts, T.E. and L.E. Olson.  ComPairWise...

_E_x_a_m_p_l_e_s:

     #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)

