VaiPhy

Simulate the synthetic datasets:

python simulate_datasets.py

Run VaiPhy with default parameters:

python main.py --dataset data_seed_1_taxa_10_pos_300

Prepare contents for post-sampling:

python post_analysis_prep.py --dataset data_seed_1_taxa_10_pos_300

Run post-sampling CSMC:

python post_sampling/csmc.py --dataset data_seed_1_taxa_10_pos_300

or

python post_sampling/csmc.py --dataset data_seed_1_taxa_10_pos_300 --csmc_n_particles 2048 --csmc_distortion_poisson_rate 4