 ======================= DARC program README file ==========================

Extract the executables by first typing "gunzip darc1.0.6_i86linux64.tar.gz" and 
then "tar xvf darc1.0.6_i86linux64.tar" This will create the directory 
'darc1.0.6_i86linux64', which contains the darc and sbsmpl_dca programs.  To
create a cma-formatted MSA as input go to the MAPGAPS website 
   http://www.igs.umaryland.edu/labs/neuwald/software/mapgaps/
and download mapgaps.  Type 'darc' or 'sbsmpl_dca' on the command line shows 
usage and input and output file descriptions.

These programs have been tested under the following Linux operating systems: 
RedHat version 7.6, and Ubuntu version X.X.  No non-standard hardware
is required and the program needs no installation requirements other than placing
the executable on a user's path. This program and the source code are freely 
available under the MIT License (see LICENSE file).

Extract the source code by first typing "gunzip darc_src_1.0.6.tar.gz" and 
then "tar xvf darc_src_1.0.6.tar" This will create the directory 'darc_src_1.0.6', 
which contains several subdirectories.  

 --------------------- Demo in example subdirectory ----------------------
To perform DARC and sbsmpl_dca analyses of C-type lectin domains go into the 'example/' 
subdirectory and type './run_example'.  This example, which includes a minimal 
subsampling option, should take about 10 minutes to finish on a typical Linux 
workstation (or less time without subsampling). From the input multiple 
sequence alignment (MSA) file (C_Lectin.mma), DARC produces the following 
output files:

C_Lectin.chk:	checkpoint file for additional analysis using our BPPS program.
C_Lectin.hsw:	sequence weights (to reduce redundancy).
C_Lectin.paths: paths to pdb coordinate files for PyMOL scripts.
C_Lectin.sprs:	SIPRIS input file (see reference 4 in usage).
C_Lectin_1.pml: pymol script for proteins of known structure included in foreground MSA.
   :     :       :     :      :     :     :     :     :      :        :    :        :
C_Lectin_8.pml:  :     :      :     :     :     :     :      :        :    :        :
C_Lectin_aln.rtf: rich text format 'contrast alignment' showing BPPS-defined patterns.
C_Lectin_fg:	query family (foreground) MSA (in cma format) as defined by BPPS
C_Lectin.darc:	summary of the results.

Temporary files:
C_Lectin_fg.in:	query MSA in PSICOV format for DCA analysis:
C_Lectin_fg_X.dca: CCMpred output file (input for STARC).
C_Lectin_fg_X.mst: STARC input file.
C_Lectin_fg_X:	EVcouplings formated DCA file (required by STARC).

 --------------------- Reproducing the published analysis ----------------------
To reproduce the analysis in the DARC paper, with slight variation due to DARC's stochastic 
nature, download darc_data.tar.gz, then, within the darc1.0.6 directory, uncompress and 
extract from darc_data.tar.gz the directory 'data'.  Go into the data subdirectory and 
type 'run_gdp' (for the gamma + delta prime versus other AAA+ analysis) or 'run_gmm' 
(for the gamma versus delta prime analysis).  Run the script 'run_gdp_sbsmpl' script 
to reproduce the subsampling analysis.  Note that this analysis requires quite a bit of RAM.

 ******************************************************************************************
    Copyright (C) 2019 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 2183
         Baltimore, MD 21201
         Tel: 410-706-6724; E-mail: aneuwald@som.umaryland.edu
 ******************************************************************************************

