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Iterative 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 jruan@cse.wustl.edu

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

Contents of the package:
   /bin: after installation, this directory includes two programs  
      - ilm, predict from a score matrix 
      - ilm_single, predict for a single sequence
   /data: this directory contains the sequence data for testing
   /src: this is where the source code resides. 
   /util:after installation, this directory includes 4 programs 
      - mixy, compute a mutual information score matrix from a multiple sequence alignment
      - hlxplot, compute a helix plot score matrix from a sequence alignment
      - makegraf, combine two score matrices together. 
      - toxrna, given a output file of the program ilm for a sequence alignment, remove gaps and get the base-pair list for a specified sequence only
      Source code of these 4 programs were obtained from J.E. Tabaska.
   /vienna: this directory includes the header files and implementations of the partition function algorithm from the Vienna Package. After installation, a library file RNAlib.a will be created in the subdirectory `lib' and is used by the program ilm_single. These files were downloaded from http://www.tbi.univie.ac.at/~ivo/RNA/.

To install:
	- in general you only need to type in "make all" from the root directory of this package. This will first compile the RNAlib library provided by the Vienna RNA package, which is needed by the ilm_single program for single sequences, and then compile the ilm and some utility programs. 
        - if you already have Vienna RNA package installed, you can go to the directory `src' and change the -I and -L options in the makefile to reflect the location of the header file and library file, and then type `make all' in that directory.
        - you may also want to go to subdirectory `src' and `vienna/lib' to change the CC, BIN, UTIL and VIENNA variables to suit your system. 

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