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.

This week(7.15-7.21)

  • Write test for ParsimonyScorer;
  • Implement NNI(Nearest Neighbor Interchanges) algorithm.