This software is under this license:

===========================================================

    Copyright (C) 2007 Piero Fariselli

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.

    PHMM lib Copyright (C) 2007  Piero Fariselli
    contacts: Piero Fariselli
              e-mail: piero@biocomp.unibo.it, piero.fariselli@unibo.it
              Dept. of Biology
              University of Bologna
              via Irnerio 42
              40126 Bologna
              Italy
    This program comes with ABSOLUTELY NO WARRANTY; for details type psCoils.py.
    This is free software, and you are welcome to redistribute it
    under the condition of preserving this text
===========================================================

#--------------------------------------------------------------------------------#
# 				REQUIREMENTS                                     #
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#     !!!!!!!   You need python2.x installed and the numpy package.  !!!!!!!     #
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TO RUN just type:

$ pred.py file.in

where file.in must contains the protein sequence in the form
of protein profile. Each line is one sequence position
and the order of the profile is:
# the order of the 20 symbol is : V L I M F W Y G A P S T C H R K Q E N D


The output consits of two lines:
the first line assign probability to contain a coiled-coil segment. 
The second line assign a putative prediction in which the symbol 'H'
represent possible coiled-coil positions.
However, the probability must be also taken into account.

Please for any use of this software cite the paper: 
Bartoli L, Fariselli P, Krogh A, Casadio R (2009) 
-CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information- Bioinformatics 25:2757-2763 (2009)