phylogenetics

Algorithms and datastructures for phylogenetics
README

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.

Install
Published
19 Mar 2022
Sources
phylogenetics-0.1.0.tbz
sha256=266c844b52074cf85b83e309ce18f4a030e36e68fd0806ee45f004f8256d9418
sha512=8ca329483c32f420b18425da04cf56d1d4c7263b463a61f42b3a99fb3cea298e04ac6d1545c8fff209e361479b566e6c086a200c96c7153751a0071bd9fcc4fb
Dependencies
printbox
< "0.6"
lacaml
>= "10.0.2"
dune
>= "2.7.0"
core
>= "v0.14.0" & < "v0.15"
biocaml
>= "0.8.0"
alcotest
with-test
Reverse Dependencies