I was working on my future job and a bioinformatics course during last two weeks. So only few things have been finished. While, everything now works as plained, as I finished the NJ algorithm one week ahead of original schedule.
Last Two Weeks(7.1-7.14)
- Solved all problems about parsimony method with the help of Mark and redesigned all classes for this algorithm;
- Implemented generic ParsimonyScorer accepting a scoring matrix for calculating parsimony score given a tree and an alignment.
- Write test for ParsimonyScorer;
- Implement NNI(Nearest Neighbor Interchanges) algorithm.