Code for experiments

• Calculate pairwise similarities with alignments/fulldataset/allVsAllAlign.m
• For the inner loop, use runFullDatasetInnerLoop.py
• For the outer loop, use runFullDatasetOuterLoop.sh scores/directory

• Download the CAFA3 data from http://biofunctionprediction.org/cafa/
• Parse the data with createCafaTrainingSet.py and createCafaTestSet.py
• Calculate pairwise similarities with alignments/fulldataset/cafaAlign.m
• For training a method, use runCafaTrain.py
• For evaluating, use runCafaTest.sh

python2, numpy, scipy, scikit-learn, matplotlib, pickle, matlab Bioinformatics toolbox