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# TARGETS : bin/dca (version 1.1)
# AUTHOR  : Jens Stoye
# DATE    : 07/1997 (v1.0); 06/1998 (v1.1)
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USAGE

dca

  [-q]             quiet (batch) modus (default: interactive modus)
  [-g]             penalize end gaps as internal gaps (default: free shift)
  [-a]             use approximate cut positions (default: C-optimal positions)
  [-o]             suppress output about progress of the program
  [-b (B|wf_file)] weight intensity (default: 0.0) or weight factor file
  [-t [order]]     tree-based or manual sequence order (default: longest first)
  [-c cost_file]   cost matrix file (default: depends on sequences)
  [-l L]           recursion stop size (default: 30)
  [-w W]           window size (default: 0)
  [-f F]           output format 1(aln), 2(fasta), 3(nex), 4(dca) (default: 2)
  <sequences>      (mandatory)


INSTALLATION

Simply type

  make

in the dca directory.

For an execution of DCA, the alignment program MSA 2.1 has to be executable in
the working directory. It can be obtained from URL

  http://fastlink.nih.gov/pub/msa/

Remark: For running MSA 2.1 (and hence DCA) with more than 10 sequences, you'll
have to increase the value of the constant NUMBER in defs.h and then recompile
the program. Also, Knut Reinert experienced that setting the value of EMAX in
ecalc.c to 99999 (rather than 50) improves the behavior of MSA 2.1 without
slowing down the program very much.
 
To test your installation of DCA, run:
 
  bin/dca -q -c cost/blosum62 seq/default.seq
 
 
ENVIRONMENT

DCA_SEQS_DIR  default directory for sequences (optional)
DCA_COST_DIR  default directory for cost matrices (optional)

You might also want to include the dca/bin directory in your PATH.


FURTHER INFORMATION

For further information see the DCA WWW Home Page on the 
Bielefeld Bioinformatics Server: 

             http://bibiserv.TechFak.Uni-Bielefeld.DE/dca/

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