phylodeep 0.0.52

Phylodynamic paramater and model inference using pretrained deep neural networks

Phylodeep

Phylodeep is a python library for parameter estimation and model selection from phylogenetic trees, based on deep learning.

Installation

Use the package pip to install phylodeep.

Usage

import phylodeep
from phylodeep import BD, BDSS, BD_vs_BDEI, BD_vs_BDSS, SUMSTATS, FULL

path_to_tree = './tests/Zurich.trees'

# set presumed sampling probability
sampling_proba = 0.20


# model selection
model_BD_vs_BDEI = phylodeep.modeldeep(path_to_tree, sampling_proba, model=BD_vs_BDEI, vector_representation=FULL)
model_BD_vs_BDSS = phylodeep.modeldeep(path_to_tree, sampling_proba, model=BD_vs_BDSS, vector_representation=FULL)

# selected models are BD and BDSS


# parameter inference
inference_param_BD = phylodeep.paramdeep(path_to_tree, sampling_proba, model=BD, vector_representation=FULL)
inference_param_BDSS = phylodeep.paramdeep(path_to_tree, sampling_proba, model=BDSS, vector_representation=FULL)

Citation

Contributing

License