package phylogenetics

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Algorithms and datastructures for phylogenetics

Install 

dune-project
 Dependency

github.com Readme Edit opam file Versions (4)

Authors

  1. L
    Louis Duchemin
  2. V
    Vincent Lanore
  3. P
    Philippe Veber

Maintainers

  1. P
    philippe.veber@gmail.com

Sources

phylogenetics-0.3.0.tbz
sha256=de867d7cc017a8e434dab43ef16f0f6495973892cd7b6a8446b18e79393704a8
sha512=0209538caf94be47eabcaa25399c54849bd4fa0fc79e0579acee27f46ef3b72aa50e17bdb48fed8e86674d4caee6c1c4c423833a2757db12e2a6cc28234510de

Description

Tags

bioinformatics evolution phylogeny

Added to opam-repository:

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. ppx_deriving
  4. menhir
  5. lacaml >= "10.0.2"
  6. yojson >= "1.6.0"
  7. gsl
  8. dune >= "3.6"
  9. core >= "v0.16.0"
  10. biotk >= "0.2.0"
  11. binning
  12. angstrom-unix

Dev Dependencies (2)

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

Optional Dependencies

None

Used by

None

Conflicts

None

Build status

Results of building phylogenetics with each compiler on check.ci.ocaml.org, run of against opam-repository 7cdc698. All results for this package.

Each result links to its build log. To keep crawlers from overloading the site, build logs require a GitHub sign-in (see ocurrent/opam-health-check). On your first log, GitHub asks you to “Authorize opam-health-check”, the OCurrent app that runs these checks; it sees only your public profile, not your repositories. The sign-in lasts 30 days.

Version OCaml 4.11 OCaml 4.14 OCaml 5.2 OCaml 5.4 OCaml 5.5
0.3.0 (this version) n/a good good good good
0.1.0 good good n/a n/a n/a
  • good Package successfully built
  • partial One of the dependencies failed to build
  • bad Package failed to build
  • n/a Package is not available in this environment
  • internal Internal failure