Infernal - inference of RNA secondary structure alignments
Sean Eddy, HHMI/Washington University in Saint Louis.

This is rudimentary code intended to document the paper "A memory
efficient dynamic programming algorithm for optimal structural
alignment of a sequence to an RNA secondary structure", SR Eddy, BMC
Bioinformatics, 3:18 (2002).

For documentation, including installation instructions and a tutorial,
see the Infernal User's Guide: Userguide.pdf.

For copyright and licensing information, see the files COPYRIGHT and
LICENSE.

To quickly build and test the software:
	./configure
	make
        make check
(But see Userguide.pdf for more installation information.)

To peruse the source code:
	it's in the src/ subdirectory.
	The covariance model structure is in structs.h
	Model construction code is in modelmaker.c
	The divide and conquer algorithm is in smallcyk.c

To run examples:
	The data used to generate Table 1 in the paper are in the 
	intro/ subdirectory.
	To gather the SSU data, for example (deal with path issues yourself; 
        executables are in the binaries/ subdir after a "make"):

	% cmbuild ssu.cm ssu.sto              [Builds model from alignment.]
        % cmscore --smallonly ssu.cm ssu.fa   [Parses/aligns E. coli SSU]
        % cmscore --scoreonly ssu.cm ssu.fa   [Scores SSU]

SRE, Wed Apr  2 18:13:28 2003 [St. Louis]


