******* Illustrative examples *******

The Ilustratives_Examples folder contains two folders: Inputs and Outputs. Each of them includes a folder with the corresponding input and output files for every studied example.

* Inputs folder * 
Contains the multiple sequence alignment, the template structure and the main input file Settings.txt required to run ProteinModelerABC.

* Outputs folder * 
Contains two folders per example. ABCOutputs includes all the files used to run ProteinModelerABC and the corresponding output files. SimulationOutputs includes all the output files produced by ProteinModelerABC for the corresponding analysis.


******* ProteinModelerABC validation results *******

The ProteinModelerABC_Validation folder includes two folders: MethodData and TestData.

* MethodData folder * 
Contains a file with the confusion matrix for every studied scenario: number of simulations (10,000, 50,000, 100,000), ABC tolerance (0.005, 0.01, 0.05) and ABC estimation method (rejection “rejection”, multinomial logistic regression “mnlogistic” and neural networks “neuralnet”).

* TestData folder *
Contains a file for the 100 results, for every studied scenario: number of simulations (10,000, 50,000, 100,000), ABC tolerance (0.005, 0.01, 0.05), ABC method (rejection “rejection”, multinomial logistic regression “mnlogistic” and neural networks “neuralnet”) and substitution model of protein evolution (Dayhoff, site-dependent Fitness SCS and site-dependent Neutral SCS models as true models).

