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
- Maintainers
-
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