Changed chooseAlignment to boolean chooseFilteredAlignment() indicating wether or not to use the filtered MSA. - Simplifies usage in runPhyloFun.R
Included new MSA filtering into runPhyloFun.R
F-Score evaluation now only regards predicted GO terms as false positives if they are not a parent term of the reference terms.
Evaluation function fScores automatically opens and closes a database connection to the Gene Ontology. Also included a function to check identity of two MSAs (Still missing testing).
Merge remote-tracking branch 'origin/master'