Moved old reults into a bak directory
Gave aa.rb --parse option an "all" option which parses all mlc files in codeml/aa_input and runs the parse script on each of them
no changes .. just removing spaces
Added FastaFile class for manipulating supplied Fasta files
Working on converting fasta files to .aa files and renaming
Started work on working out correct attributes to pass to control file
G Clock and non clock versions of controlfile being auto-generated
moving tree files + renaming. Also wrote a function to compare 2 files.