Started merging PhyloFun_Rcpp and pure R implementation. Making a proper R package
Finished DESCRIPTION including dependencies
Added version to the packages PhyloFun DEPENDS on
Shorthand for License
Added directory 'inst' in which all test data files are stored
Moved all 'executable' Rscripts into new directory exec
Added rcpp_phylo_fun
Replacing old R functions with new Rcpp ones
PhyloFun is now running with the new Rcpp generation of the bayesian conditional probability tables.

PhyloFun is now a "true" R package and can be installed with R CMD INSTALL PhyloFun/
Moved some files around and added Description and Namespace files.
Also debugged some functions that accessed members of XStringSet, somehow on debian the functions worked but on Mac OS X not. Had to use the double square bracket accessor and length on S4 class AAString instead of nchar and converting it to character vector of length 1…

Still missing:
 * remove project.file.path calls in all scripts.
 * adjust exec scripts to require PhyloFun and if needed load PhyloFun's data
 * Move all tests into test functions
 * Generate Rdoc from the functions comments. Maybe by using Vim macros.
Added some helpful installation and how-to run documentation
Used better -more "default"- command line args for PhyloFun call
Git now ignores C++ *.so and *.o
Merge remote branch 'origin/rcpp' into rcpp
Added doc about how to set number of threads used by FastTreeMP (OpenMP)
Corrected typo in documentation…
Rewrote function to count or extract protein pairs from a large sequence similarity search result table.
Added function to select parent GO terms of argument GO level (distance to GO DAG's root node).
Debugged new SQL function to select GO term parents of argument GO level.
Debugged naming of function local object.
Debugged function to find parent GO term of specific distance to GO DAG root and introduced function to generate GO profiles as annotation frequencies of parent GO terms of certain level ( default is 3 ).