package phylogenetics

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Algorithms and datastructures for phylogenetics

Install

Dune Dependency

Authors

Maintainers

Sources

phylogenetics-0.1.0.tbz
sha256=266c844b52074cf85b83e309ce18f4a030e36e68fd0806ee45f004f8256d9418
sha512=8ca329483c32f420b18425da04cf56d1d4c7263b463a61f42b3a99fb3cea298e04ac6d1545c8fff209e361479b566e6c086a200c96c7153751a0071bd9fcc4fb

Description

Tags

bioinformatics evolution phylogeny

Published: 19 Mar 2022

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 (9)

  1. printbox < "0.6"
  2. ppx_deriving
  3. menhir
  4. lacaml >= "10.0.2"
  5. gsl
  6. dune >= "2.7.0"
  7. core >= "v0.14.0" & < "v0.15"
  8. biocaml >= "0.8.0"
  9. angstrom-unix

Dev Dependencies (1)

  1. alcotest with-test

Used by

None

Conflicts

None