Programs for BPPS/SIPRIS analysis of protein domains.

For further information contact:
 Prof. Andrew F. Neuwald
 Institute for Genome Sciences and
 Department of Biochemistry & Molecular Biology
 University of Maryland School of Medicine
 801 West Baltimore St.
 BioPark II, Room 617
 Baltimore, MD 21201
 Tel: 410-706-6724; Fax: 410-706-1482
 E-mail: aneuwald@som.umaryland.edu

To compile the code simply type "./mkdrivers" within the src_code/ directory. This will
	create executables within the src_code/bin/ directory. WARNING: lex and yacc 
	must be on your path for code compilation. If only flex and bison are available,
	then symbolic links (lex --> flex and yacc --> bison) may be set up instead.

Literature references:
1. Neuwald, A.F. 2009. Rapid detection, classification and accurate alignment of up to
        a million or more related protein sequences.  Bioinformatics 25: 1869-1875
        (Describes an initial version of the MAPGAPS program.)

2. Neuwald, A.F. 2011. Surveying the manifold divergence of an entire protein class for
        statistical clues to underlying biochemical mechanisms.  Statistical Applications
        in Genetics and Molecular Biology 10(1): Article 36. (30 pages)
        (Describes a basic version of BPPS sampling).

3. Neuwald, A.F. 2014. A Bayesian sampler for optimization of protein domain hierarchies.
        Journal of Computational Biology 21(3): 269-286.
        (Describes the first step in the BPPS sampler used here).

4. Neuwald, A.F. 2014. Protein Domain Hierarchy Gibbs Sampling Strategies. Statistical
        Applications in Genetics and Molecular Biology 13(4):497-517.
        (Describes statistical aspects of BPPS sampling).

5. Neuwald, A.F., L. Aravind & S.F. Altschul. 2017. Inferring Joint Sequence-Structural
        Determinants of Protein Functional Specificity. eLife In revision.
	(Describes BPPS/SIPRIS analysis using the mapgaps, bpps & sipris programs.)