Phylodynamic paramater and model inference using pretrained deep neural networks
Project description
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
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
phylodeep-0.0.5.tar.gz
(11.3 kB
view hashes)
Built Distribution
Close
Hashes for phylodeep-0.0.5-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | b1d3f5a17a89f1f64f86bde99163337c295e3c145cc571c5988ff2129f628256 |
|
MD5 | 0c24963a319572e5203c4ccd72e8de8f |
|
BLAKE2b-256 | fe44a4386ac21238bed6f9207ac5d9061ab61da03c9e7d57c23cd7bf5475c5e0 |