# There are four directories: bin, DETECTER, data and doc

# /bin contains the main script: DETECTER.pl
# To run the code, type the following command from the /bin directory
perl DETECTER.pl inputfilename

# To save the output to a file, do the following:
perl DETECTER.pl > myoutput.txt

# If no inputfilename is given, the program will take ABC.Redo.CFTRsubtree.Crop.txt 
# as a defaulft input.  This file is located in the /data directory

# /DETECTER contains three modules: Node, NodesBlock and Site

# /data contains two sample input files and the corresponding output files

# /doc contains the auto-generated html code to display documentation.  To generate this 
# documentation (already done... no need to do it again)  run this command from PAML_dir/bin to
# generate web based documentation.  To look at this documentation, simply open index.html
perl ~/Programs/pdoc-1.0/scripts/perlmod2www.pl -source ../DETECTER/  -target ../doc
# To view the help files open doc/index.html in any web browser

Description of the script

This script parses a PAML input file.  The script locates the
probability distribution at each node, by site, and stores the node
number, the site of the alignment, the extant sequence and a list of
posterior probabilities and their associated amino acids.  The script
then combines all of the extant sequences for each node, by site, and
removes the redundancies.  Similarly, all of the posterior
probabilities and their associated amino acids are combined and the
redundant amino acids are removed.  In the case of the posterior
probabilities, however, amino acids are maintained only if the
posterior probability is greater or equal that 0.05.  The output of
this script contains the header "Prob distribution at node xxx, by
site" for all of the nodes followed by 3 columns: the site of the
alignment, a list of tolerated residues (those not resulting from the
extant sequence are in lower case), and a list of non-tolerated
residues.