package phylogenetics

  1. Overview
  2. Docs
Algorithms and datastructures for phylogenetics

Install

Dune Dependency

Authors

Maintainers

Sources

phylogenetics-0.2.0.tbz
sha256=245a58a77a725bb3eb063a82c300d9c6424f03ce1da7a42cf2b38fbc73d8f76a
sha512=cf0c5ce2d67941331b35c018cef9db51cb3664b539f70b098a96961d8dc597f56f4f28a6db6663524245b7afded21969848ea157ae53759675b7bdf7c96e133a

Description

Tags

bioinformatics evolution phylogeny

Published: 15 May 2023

README

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.

Dependencies (12)

  1. printbox-text
  2. printbox >= "0.6.1"
  3. yojson
  4. ppx_deriving
  5. menhir
  6. lacaml >= "10.0.2"
  7. gsl
  8. dune >= "3.6"
  9. core >= "v0.15.0" & < "v0.16"
  10. biotk >= "0.2.0"
  11. binning
  12. angstrom-unix

Dev Dependencies (2)

  1. odoc with-doc
  2. alcotest with-test

Used by

None

Conflicts

None

OCaml

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