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