AlignmentProcessor1.0

Added ability to change KaKs_Calculator run modes.
Added ability to retain temporary files from CodeML and PhyML.
Added example CodeML control files for null and alternative models for branch site, branch specific, and pairwise analyses.
CodeML control files no longer need to be named "codeml.ctl"; instead, they only need to have a ".ctl" extension.
Fixed bug causing the program to crash if no forward branch was specified.