+++ /dev/null
-
- PROBCONS
- ~~~~~~~~
-
- Probabilistic consistency-based multiple sequence alignment
-
------------------------------------------------------------------
-
-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.
-
------------------------------------------------------------------
-
-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.
-
------------------------------------------------------------------
-
-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)
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