AlignmentProcessor0.10

Added capabilty to run CodeML on multiple threads.

AlignmentProcessor0.9

Any script that removes sequences or files will now produce a log.
If CodeML runmode is set to 0 or 1, 07_CodeMLonDir.py will call the ape R package to dynamically trim trees for each gene.
seqDict function now stores sequences in an ordered dictionary to preserve the order of the original alignment file.

AlignmentProcessor0.8

The program will now remove sequences with premature stop codons by default, and will produce a list of all genes which contained them.
The program will now produce error messages if the wrong file conversion is used for an analysis or if KaKs_Calculator or PAML are not installed in the proper directories.
The 02_namesList.txt file can now be printed to the terminal via the command line and new entries can be appended to it.

AlignmentProcessor0.7

Added Windows and Mac KaKs_Calculator binaries.
Updated the RadMe and incorporated some minor streamlining.

AlignmentProcessor0.6

Beta release