(MOCASSIN-prot Pipeline)
(README: last updated on May 27, 2016)

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TESTED:
Linux
MacOS X
Windows 7
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Before using the pipeline programs, the following must be installed on the system:

1. HMMER3 version 3.1 or newer (tested with version 3.1) must be installed on the system
2. BLAST program suite must be installed on the system (tested with version 2.2)
3. MATLAB (tested with version 2015b)
   *If using MATLAB version 2013 or older you will need to change some lines in the MATLAB scripts mocassin_prot.m (see individual README for mocassin_prot.m for details).
4. MATLAB Optimization and Parallel Computing Toolboxes
5. A Perl interpreter is needed to run mtxassemble.pl, which prepares the input scoring matrices from the protein sequences.


The following four scripts are included. The description of each script is found in the "Individual_Script_Readmes" directory.

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1. Scoring Matrix Creation:
   mtxassemble.pl
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2. Solving Optimization Problems (for primary network):
   mocassin_prot.m
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3. Creating Cytoscape Input File (for network visualization)
   make_cytoscape_file.m
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4. Solving Optimization Problems (for higher order networks)
   mocassin_prot_iter.m
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