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README.CDEPP.md

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This is the implementation of C-DEPP

https://www.biorxiv.org/content/10.1101/2023.03.27.534201v2

Install

pip install depp==0.3.1

Usage

Training

example
train_cluster_depp.sh -t test/cluster_depp/backbone.nwk -s test/cluster_depp/backbone.fa -g 2 -o outdir

  • -t tree file
  • -s sequences file
  • -g gpu id. If no gpu is used, use -g nogpu, default 0
  • -o output directory
  • -e number of training epochs, default 2000.

Testing

example
depp_distance.py seqdir=outdir/test_seqs_add_repr query_seq_file=test/cluster_depp/query.fa model_path=outdir/cluster-depp.pth outdir=outdir use_multi_class=True prob_thr=200
This will produce distance files in directory outdir named depp*csv