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
###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
# 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
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