Metadata-Version: 2.1
Name: phylodeep
Version: 0.0.64
Summary: Phylodynamic paramater and model inference using pretrained deep neural networks
Home-page: https://github.com/evolbioinfo/deepphylo
Author: Jakub Voznica, Anna Zhukova
Author-email: jakub.voznica@pasteur.fr
License: UNKNOWN
Keywords: deepphylo,deepparam,deepmodel,phylodynamics,deep learning,model selection,phylogeny,molecular epidemiology
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Classifier: Topic :: Software Development
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Description-Content-Type: text/markdown
Requires-Dist: ete3
Requires-Dist: pandas
Requires-Dist: numpy (==1.18.5)
Requires-Dist: scipy
Requires-Dist: sklearn
Requires-Dist: tensorflow
Requires-Dist: joblib (==0.13.2)

# Phylodeep

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

## Installation

Use the package [pip](https://pip.pypa.io/en/stable/) to install phylodeep.

## Usage 

###Python

```python
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)

```

###Command line
```python
paramdeep -t ./tests/Zurich.trees -p 0.25 -m BDEI -v FFNN_ -o trial.csv

```



## Citation


## Contributing


## License

