package phylogenetics

Phylogenetics

This library provides algorithms and datastructures to perform inferences in molecular evolution. It features:

• typed representation of DNA/amino-acid/codon alphabets
• rate matrices and probability transition matrices for various evolution models (JC69, K80, GTR, Mutsel)
• site-independent Gillespie simulators
• a simulator for gapped alignments under the TKF91 model
• a tree simulator under the birth-death model
• parsers for Newick, NHX and phylip formats
• a GSL-based implementation of the pruning algorithm, with underflow avoidance

Installation

Using opam, simply type

opam install phylogenetics

to install the library, or:

opam pin add -y phylogenetics --dev-repo

to get the current development version.