PsiPartition

This is the official implementation of the paper "PsiPartition: Improved Site Partitioning for Genomic Data by Parameterized Sorting Indices and Bayesian Optimization" Journal of Molecular Evolution.

Installation

conda create -n PsiPartition
conda activate PsiPartition
pip install -r requirements.txt

To enable the Bayesian optimization, you need to register an account on Weights & Biases.

PsiPartition was tested with the version of IQ-TREE 1.6.12. Please download IQ-TREE and decompress it. Make sure PsiPartition can find iqtree binary on the path ./ThirdParty/iqtree-1.6.12-Linux/bin/iqtree.

Usage

python PsiPartition_wandb.py --msa <MSA File> --format <fasta or phylip> --alphabet <dna or aa> --max_partitions <max_partitions> --n_iter <number of iterations>

Help

If you have any questions, please contact me at shijie.xu@ees.hokudai.ac.jp.