Updated version info for 1.6

Automated filetype and analysis selection.

Allows user supplied phylogenic tree.

Changed extensions for overview readmes.

Parallelized PhyML, retains temp files, reuses tree files.

Reformatted README.md

Added Branch specific and pairwise null and alternative control files.

Added python script to convert fasta to axt, streamlined i/o.

Removed extra readme

Streamlined code