cleanup to documentation

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phrapl@230 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
tweaks to improve functionality

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phrapl@231 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
moved unneeded functions into here

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phrapl@232 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
added data

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phrapl@233 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
fixed imports issues

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phrapl@234 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
compressed data

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phrapl@235 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
reorganization

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phrapl@236 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
better path to installed version of compareClades

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/phrapl@237 edb9625f-4e0d-4859-8d74-9fd3b1da38cb