├── .developer └── how_to_debug_FRACTAL.md ├── .gitignore ├── FRACTAL ├── LICENSE ├── README.md ├── UpdateLog.md ├── example ├── output │ ├── FRACTAL_ML.nwk │ ├── FRACTAL_NJ.nwk │ ├── FRACTAL_edit.nwk │ ├── FRACTAL_raxml.nwk │ ├── FRACTAL_unaligned.nwk │ └── FRACTALout.nwk ├── script │ └── ml_raxml.sh ├── test.edit ├── test.fa ├── test.nwk └── test.unaligned.fa ├── images ├── .DS_Store ├── fractal_concept.jpg └── fractal_unaligned.jpg ├── python ├── FRACluster.new.py ├── TreeAssembly.py ├── divide_ref_and_query.py ├── error_process.py ├── extraction.py ├── jplace_parse.py ├── manage_edits.py ├── partition.py ├── partition_sequences.py ├── placement.py ├── rename_sequence.py └── transform.py └── shell ├── SUPERVISE.sh └── TREE.sh /.developer/how_to_debug_FRACTAL.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yachielab/FRACTAL/HEAD/.developer/how_to_debug_FRACTAL.md 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