======================= STARC README file ==========================

Extract the STARC program, the examples in the paper, and the C++ source code by 
first typing "gunzip /starc_v1.0.4.tar.gz" and then "tar xvf /starc_v1.0.4.tar". 
This will create the directory '/starc_v1.0.4', which contains various 
subdirectories.

 --------------------- Sample STARC analyses ----------------------
To run STARC on the proteins described in the corresponding manuscript go 
into the '/starc_v1.0.4/' directory and type './run_all '.  The output will
appear as *.out files in each of the subdirectories.
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 --------------------- compiling the code ----------------------
To compile the source code go into the code directory and type './mkstarc'. 
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The 'bin' subdirectory contains the STARC and Wilcoxon programs.  These were
compiled under a RedHat 5.11 Linux operating system (kernelrelease 2.6.18-419.el5)
running on an Intel Xeon x86_64 machine.

The following DCA programs were used to generate DCA scores for the analyses:

   CCMpred (https://github.com/soedinglab/CCMpred)
	Seemayer S, Gruber M, Söding J. "CCMpred--fast and precise prediction of 
	protein residue-residue contacts from correlated mutations." 
	Bioinformatics. 2014 30(21):3128-30. PMID: 25064567
   EVcouplings (http://evfold.org/)
	Marks DS, Colwell LJ, Sheridan R, Hopf TA, Pagnani A, Zecchina R, Sander C.
	"Protein 3D structure computed from evolutionary sequence variation". 
	PLoS One. 2011;6(12):e28766. PMID: 22163331.
   GaussDCA (http://areeweb.polito.it/ricerca/cmp/code)
	Baldassi C, Zamparo M, Feinauer C, Procaccini A, Zecchina R, Weigt M,
	Pagnani A. (2014) "Fast and accurate multivariate Gaussian modeling of
	protein families: Predicting residue contacts and protein-interaction
	partners". PLoS ONE 9(3): e92721. PMID: 24663061.
   PSICOV (http://bioinf.cs.ucl.ac.uk/downloads/PSICOV)
	Jones DT, Buchan DW, Cozzetto D, Pontil M. (2012) "PSICOV: precise
	structural contact prediction using sparse inverse covariance estimation
	on large multiple sequence alignments". Bioinformatics. 2012 28(2):184-90. 
	PMID: 22101153.

The input DCA files need to be in EVcouplings, GaussDCA or PSICOV formats. If GaussDCA or PSICOV
formats are used, then the protein sequence corresponding to the structure also needs to be 
provided (see the starc program usage & pcv_gsf_format/ directory). To serve as input, CCMpred 
DCA files need to be converted into one of these three formats; alternatively, a modified 
version of CCMpred is provided (bin/ccm) that will produce output in PSICOV format.

 ******************************************************************************************
    Copyright (C) 2018 Andrew F. Neuwald, The University of Maryland School of Medicine.

    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
    INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
    PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL THE AUTHOR OR COPYRIGHT HOLDERS BE
    LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT
    OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
    OTHER DEALINGS IN THE SOFTWARE.

    For further information contact:
         Andrew F. Neuwald
         Institute for Genome Sciences and
         Department of Biochemistry & Molecular Biology
         University of Maryland School of Medicine
         670 West Baltimore St.
         HSF III, Room 3053
         Baltimore, MD 21201
         Tel: 410-706-6724; E-mail: aneuwald@som.umaryland.edu
 ******************************************************************************************