Last Week(6.24-6.30)

  • Implemented the UPGMA and NJ algorithms(DistanceTreeConstructor) by porting my Java code for those two.
  • Added test code in test_TreeConstruction for both algorithms

This week(7.1-7.7)

  • Get more clear understanding of the parsimony methods for both DNA and protein sequences.
  • Design the parsimony score method and write document and tests for it;
  • Implement method to calculate the parsimony score for a given tree and an alignment;

DistanceTreeConstructor Usage

    from Bio import AlignIO
    from Bio.Phylo.TreeConstruction import DistanceCaluculator
    from Bio.Phylo.TreeConstruction import DistanceTreeConstructor
    from Bio.Phylo.TreeConstruction import TreeConstruction
    aln = AlignIO.read(open('TreeConstruction/msa.phy'), 'phylip')

    calculator = DistanceCaluculator(aln, 'blosum62')
    dm = calculator.get_distance()
    constructor = DistanceTreeConstructor(dm)
    upgma_tree = constructor.upgma()
    nj_tree = constructor.nj()