Name: phylogenetics
Owner: Biocaml
Description: Algorithms and datastructures for phylogenetics
Created: 2017-12-05 15:54:02.0
Updated: 2017-12-06 08:35:56.0
Pushed: 2017-12-15 09:05:17.0
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Size: 303
Language: OCaml
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README
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