PROBCONS
                          ~~~~~~~~                          

   Probabilistic consistency-based multiple sequence alignment 

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PROBCONS is a novel tool for generating  multiple  alignments
of protein sequences.  Using a combination  of  probabilistic 
modeling and consistency-based alignment techniques, PROBCONS
has achieved the highest accuracy of all alignment methods to
date. 

PROBCONS was developed by Chuong B. Do in collaboration  with 
Michael Brudno in the research group  of  Serafim  Batzoglou,
Department of Computer Science, Stanford University.

For more information on the algorithms, please see

     Do, C.B., Brudno, M., and Batzoglou, S. (2004) PROBCONS:
     Probabilistic Consistency-based  Multiple  Alignment  of
     Amino Acid Sequences.  12th International Conference  on
     Intelligent Systems for Molecular Biology.  In press.

and

     Do, C.B., Brudno, M., and Batzoglou, S. (2004) PROBCONS:
     Probabilistic Consistency-based  Multiple  Alignment  of
     Amino Acid Sequences.  The 19th National  Conference  on
     Artificial Intelligence (AAAI-04).  In press.

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PROBCONS has been made  freely  available  as  PUBLIC  DOMAIN
software and hence is not subject to copyright in the  United
States.  This system and/or any portion of  the  source  code
may be used, modified, or redistributed without restrictions.  
PROBCONS is distributed WITHOUT WARRANTY, express or implied.
The authors accept NO LEGAL LIABILITY OR  RESPONSIBILITY  for
loss due to reliance on the program.
   
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Version History

1.0, 3/23/2004 (Chuong Do)
   -- initial release

1.01, 3/25/2004 (Chuong Do)
   -- fixed error in training procedure
   -- retrained default parameters for 1 and 2 pairs of insert
      states

1.02, 4/17/2004 (Chuong Do)
   -- replaced LOG_ADD and EXP routines
   -- added support for reading MSF format files
   -- added two extra utilities for scoring PROBCONS alignments
      (for benchmarking purposes)
      -- added the "compare" program for scoring alignments
         according to a reference alignment with respect to 
         sum-of-pairs and column scores
      -- added the "fixref" program for adjusting PREFAB 
	 alignments to contain all letters of the input 
	 sequences; basically the main program for PROBCONS
         "hacked" to get the job done

1.03, 5/3/2004 (Chuong Do)
   -- added option to do all-pairs pairwise alignments instead
      of constructing a full multiple alignment
   -- added support for reading DIALIGN style files
   -- enabled support for using BAliBASE annotations for scoring
      BAliBASE alignments
   -- several minor bug fixes thanks to Bob Edgar
   -- added "project" program to project multiple alignment to
      pairwise alignments

1.04, 5/9/2004 (Chuong Do)
   -- switched over to default of one-insert state pair
   -- retrained default parameters
   -- added annotation scores
   -- small changes to model topology to make end gaps symmetrical
   -- added makegnuplot utility to plot annotation scores

1.05, 5/26/2004 (Chuong Do)
   -- added cutoff filtering for posterior scores
   -- made small corrections to recurrences for computing alignments
   -- added CLUSTALW output support

1.06, 7/13/2004 (Chuong Do)
   -- ProbCons is now PUBLIC DOMAIN software.

1.07, 8/30/2004 (Chuong Do)
   -- Fixed CLUSTALW output for sequence names (thanks to John Calley
      for pointing this out)

1.08, 8/31/2004 (Chuong Do)
   -- Added option for alignment order output (-a).

1.09, 9/1/2004 (Chuong Do)
   -- PROBCONS now allows input files with existing gaps -- these are
      automatically stripped before alignment.

1.10, 3/16/2005 (Chuong Do)
   -- Reduced memory consumption by
      -- not storing posterior matrix transposes
      -- restricting consistency-derived posterior matrices to original posterior matrix

1.11, 12/1/2006 (Chuong Do)
   -- Fixed bug with conflict between --annot and -a options

1.12, 4/1/2006 (Chuong Do)
   -- Fixed GCC 4.3 compatibility problems (thanks to Martin Michlmayr and Charles Plessy)