Added #! to example_X1_plots.R
Added more comments to example_A1.R
Minor comment fixes in example_A1.R
Minor documentation fixes.
Fixed some R CMD warnings.
README fix.
One more README fix.
Updated package homepage in the DESCRIPTION file.
Merge remote branch 'greg/master'

Conflicts:
	PhyloSim.R
Fixed documentation issues for the getAlignmentLength method.
Added the 'phylosim' alias to the PhyloSim class documentation.
Relasing PhyloSim v0.13
Updated tarball name.
Removed PAML data files from package.
Tweeked the PhyloSim class examples to improve speed.
Re-releasing PhyloSim v0.13
Merge remote branch 'greg/master'
Fixed some overwrite=TRUE issues.
Vignette Makefile update.
Releasing PhyloSim v0.14