Metadata-Version: 2.1
Name: phylodeep
Version: 0.0.94
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: phylodynamics,deep learning,model selection,phylogeny,molecular epidemiology,paramdeep,phylodeep,deep learning,convolutional networks
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 (==3.1.1)
Requires-Dist: pandas (==0.23.4)
Requires-Dist: numpy (==1.18.5)
Requires-Dist: scipy (==1.1.0)
Requires-Dist: scikit-learn (==0.19.1)
Requires-Dist: tensorflow (==1.13.1)
Requires-Dist: joblib (==0.13.2)
Requires-Dist: h5py (<3.0.0)
Requires-Dist: Keras (==2.4.3)
Requires-Dist: phylodeep-data-BD-small
Requires-Dist: phylodeep-data-BD-large
Requires-Dist: phylodeep-data-BDEI-small
Requires-Dist: phylodeep-data-BDEI-large
Requires-Dist: phylodeep-data-BDSS-large

# 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

# a priori check


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

# the selected model is 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
# parameter inference
paramdeep -t ./tests/Zurich.trees -p 0.25 -m BDSS -v CNN_FULL_TREE -o HIV_Zurich_BDSS_CNN.csv
paramdeep -t ./tests/Zurich.trees -p 0.25 -m BDSS -v FFNN_SUMSTATS -o HIV_Zurich_BDSS_FFNN_CI.csv -c

# model selection


```



## Citation


## Contributing


## License

