PFORESTER
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This software is a probabilistic clone of RNAforester using Pair SCFGs.
It was primarily conceived to infer RNAforester scoring schemes by making use 
of the Expectation Maximization algorithm.
By the way, it can be used as an alternative tool to align two RNA secondary 
structures under the so called Welformed Forest Alignment model.

The primary reference point for RNAforester is the following URL:
	http://bibiserv.TechFak.Uni-Bielefeld.DE/rnaforester/

Further informations on Pforester can be found at the following URL:
	http://CeBiTec.Uni-Bielefeld.DE/~esiragus/

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INSTALLATION
============

Pforester relies on a slightly modified version of the DART library. 

1. Compile the modified dart library:
	cd dart
	make release libs  # or debug
	cd ..
	
2. Compile Pforester:
	cd Pforester/Release  # or Debug
	export DART_SRC=../../dart/src/
	export DART_LIB=../../dart/lib/
	make

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ECLIPSE
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Pforester and dart can be imported as standard Eclipse projects.

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USAGE
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- Training

1. Convert each RNA secondary structure into the FlatForest format:
	perl/convert.pl -ifile MyDataSet/RNA.ct -ofile MyDataSet/RNA.ff

2. Build a training set consisting of a random 0.1% sample of all the pairings:
	perl/trainingset.pl MyDataSet/ MyTrainingSet.ff 0.001

3. Run Pforester in training mode:
	Release/Pforester --train --affine --structure -ts MyTrainingSet.ff \
			-lp ParamSet/default-affine-structure.set -sp MyParamSet.set

4. Convert the parameter set into the Pforester scoring scheme:
	perl/paramset2score.pl --affine --structure -ifile MyParamSet.set

- Alignment

1. Convert each RNA secondary structure into the FlatForest format.

2. Build an alignment set consisting of pairs of RNA secondary structures.

3. Run Pforester in alignment mode:

	Release/Pforester --align --affine --structure -as MyAlignmentSet.ff \
			-lp MyParamSet.set > MyAlignedSet.ff

4. Convert the alignments into the Stockholm format:

	perl/flatforest2stockholm.pl MyAlignedSet.ff MyAlignedSet.stk

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