Crushing Back-Related Monkeys

I'm taking the day and crushing some annoying cludges that have been in my code for a while.

I finally made a simple utility to touch all data to make it "up-to-date". This was becoming such an annoyance since I'm updating the "processing file" all the time to add new stuff ... and since this is the "root" of the processing when it got updated then EVERYTHING needed to be redone. Now simply running the AnalysisCode.py script with the --fresh argument will update everything that exists!

I finally fixed the --processing-file argument ... before I would often have to change it in the source-file everytime I wanted to do an analysis on a different program. Now it properly respects that input argument!

Fixed the issue with large input sequences overloading muscle ... now if Muscle errors out then I rename the input file and skip it in all future runs.

Now can process multiple species files. If the AnalysisCode.py is given a --do-all parameter then it will do a DEPTH-FIRST analysis of all processing files in "importance-order". This will be useful when I

Removed the ClustalW related files since they are no longer needed.

Now the linkage files are converted to "reference space" after they are finished. These are what are then aggregated together.

Now the Tree-merging never aggregates "reference" genomes together since this will make it impossible to convert to the proper numbering scheme later!