Metadata-Version: 2.1
Name: phylodeep
Version: 0.0.2
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
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](https://pip.pypa.io/en/stable/) to install phylodeep.
        
        ## Usage 
        
        ```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)
        
        ```
        
        ## Citation
        
        
        ## Contributing
        
        
        ## License
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
