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eveGNN

eveGNN contains functions and scripts to apply Neural Network approaches on phylogenetic trees, for tree-level parameter estimation.

Dependency

  • Optuna >= 3.4.0
  • R >= 4.2.1
  • Python >= 3.8.16
  • PyTorch Geometric >= 2.4.0
  • eveGNN (in R, run devtools::install_github("EvoLandEco/eveGNN"))

How to use

ADAM (Automated DAta Manager) is a simple shell program to help manage simulation data, train GNN model and more. The program and the scripts it calls are designed for a cluster computer in the SLURM environment.

  • First, clone the repo:
git clone https://github.com/EvoLandEco/eveGNN
  • Second, locate to bash, create a folder for new project:
cd Bash
mkdir myproject
  • Finally, run ADAM:
bash ADAM.sh myproject

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