package phylogenetics

README

Currently implemented:

• topology tree data structure w/ branch length and indexes at leaves

  • parser from post-order enumeration
  • newick parser

• data structures for bases, sequences and sequence tables;

  • hashtable implem for alignments (+ legacy list implem)
  • list implem for sequences
• linear algebra functions (half wrappers around lacaml functions and half new functions);

• evolution models (w/ static distribution and transition matrix diagonalization):

  • JC69
  • K80
  • model generation from transition matrix (poor performance so far)
• felsenstein pruning w/ underflow avoidance
• sequence generation from model
• distribution plotting using gnuplot

• tests that compare results to bio++

  • interface for bppml and bppseqgen for validating test results