Inside each experiment folder the following relative paths are present. Each of them correspond to a meaningful 
subset of the data and CSMET results.

experX - the root folder where all data and results for experiment X are stored

experX/pt1 , experX/pt2 upto a maximum of experX/pt9

Each of these folders correspond to a particular experiment point, and can contain as many as 50 data points, each 
corresponding to a single run of CSMET.

experX/ptY/seq0 , experX/ptY/seq1 upto a maximum of experX/ptY/seq49 

Each of these folders contain the entire training data, testing data, simulator configuration (for simulated data), CRM 
name (for real data, in the file name.txt) and CSMET output intermediate and result files.

experX/ptY/seqZ/train  contain the training data for that run

experX/ptY/seqZ/test contain the testing data for that run

experX/ptY/seqZ/csmet_out contains CSMET output files for that run for all the simulation experiments. For real experiments, the output
can be seen at http://www.cs.cmu.edu/sailing/csmet/summary.html

experX/ptY/seqZ/train/gt and experX/ptY/seqZ/test/gt contain the ground truth (FASTA file as .FASTA, motif locations on 
forward strand as .mtf, motif locations on reverse strand for real data as .mtfr and known functional annotation as .truth

experX/ptY/seqZ/train/estim and experX/ptY/seqZ/test/estim contain estimated parameters which are fed to CSMET from the corresponding 
gt folder. These include pwm.bkg for the estimated distribution of nucleotides in background sequences, and
pwm.mtf for the motif PWM. Technically, CSMET only uses the estimated parameters from the training sequence. Estimated data
on the test sequence is provided for comparing training and test data.

experX/ptY/seqZ/train/config and experX/ptY/seqZ/train/config contain simulator configurations for 
generating the corresponding files. including the annotation_tree_params for annotation tree parameters,
motif_tree_params for motif tree parameters, bkg_tree_params for background tree parameters, tree.anno for the 
annotation tree topology and branch lengths, tree.motif for the motif tree topology and branch lengths, and 
tree.bkg for the background tree topology and branch lengths.

Inside the experX/ptY/seqZ/csmet_out folder, the following files are present :

settings.train
The settings file for the training phase

settings.test
The settings file for the testing phase

testfullmat.txt
The predicted functional annotations for the test sequence

testsummary.txt
The predicted HMM states for the test sequence