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