AlignmentProcessor v1.6

Incorporated pyfaidx to speed up fasta input/ouput

AlignmentProcessor v1.5

If the kaks or codeml flag is given, alignments will automatically be converted into axt/phylip.
ConcatenateCodeML.p.y automatically determines input type

AlignmentProcessor1.4

Fixed bug causing Exec formatting error when running CodeML on servers.
Fixed bug causing only first species in low quality alignment to be filtered out.
Writes CodeML stdout to logs in tmp folders. Stderr is printed to the screen.
Allows users to specify their own phlyogenic tree.

AlignmentProcessor1.3

01_SplitFasta.py can automatically detect Ensembl, NCBI, and Stitch Gene Blocks IDs. If another gene Id is used in the fasta headers, it will throw an error.

Progress is printed to the screen when running CodeML

PhyML is now called for each gene immediately before CodeML

Fixed bug causing CodeML to freeze

AlignmentProcessor1.2

KaKs_Calculator can be called in parallel.
PhyML can be called in parallel.
Changed “--noCleanUp” flag to “--cleanUp” so that temporary files are saved by default.

AlignmentProcessor1.1

Compressed individual scripts to reduce input/output functions, number of intermediate files generated, and improve organization.
Enabled program to automatically convert UCSC headers.
Made individual scripts more user friendly.
Included pdf ReadMe.

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.

AlignmentProcessor0.21

Replaced 06_parseFastaIntoAXT.pl with a python script to convert fasta files to axt.
Now accepts .fa and .fasta files in step 2.

AlignmentProcessor0.20

Incorporated PhyML to create unique phylogenic trees for each gene. This removes the need to provide a tree beforehand, or to trim the provided tree.

AlignmentProcessor0.11

CodeMLonDir now writes a list of completed files
pruneTree.R is no longer called recusively