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Iterated Loop Matching (ILM) for RNA Secondary Structure Prediction with Pseudoknots
(version 1.0, March 2003)

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Please send bug reports, comments etc. to zhang@cse.wustl.edu or or jruan@cse.wustl.edu

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This software package provides an implementation of the iterated loop matching algorithm (ILM) for RNA secondary structure predction with pseudoknots. It is able to predict a consensus structure for aligned homologous sequences, using combined thermodynamic and covariance information, but also able to predict for a single sequence using thermodynamic information alone.

Contents of the package:
   /bin: after installation, this directory includes two programs  
      - ilm, predict a secondary structure given a score matrix 
      - mixy, compute a mutual information score matrix from a multiple sequence alignment
      - hlxplot, compute a helix plot score matrix from a sequence alignment
      - xhlxplot, compute an extended helix plot score matrix from a single sequence or a sequence alignment
      - makegraf, combine two score matrices together. 
      - rAlign, given an output file of ilm for a sequence alignment, remove gaps and get the base-pair list for a specified sequence only
   /data: this directory contains the sequence data for testing
   /src: this is where the source code resides. 
      Source code for mixy, hlxplot, makegraf, and rAlign were obtained from J.E. Tabaska.

To install:
	- in general you only need to type in "make install" from the root directory of this package. This will compile all source code under subdirectory src and produce binary files in subdirectory bin. 
        - you may also want to go to subdirectory `src' to change the CC, and BIN variables to suit your system. 

For usage of each program:
   type the program name with option `-h' or `--help'.