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[TreeCmp](https://eti.pg.edu.pl/treecmp/index.html) v2.0\n- TMC\n\n## Installation\n\nThis will download and install TreeCmp and eSTGt:\n\n```bash\n$ ./install.sh\n```\n\n## Configuration\n\nUse a proper config file for your environment:\n\n- `config.math102-lx.env` for math102-lx\n- `config.windows.env` for Windows\n- `config.mac.env` for Mac OS X\n\nor you can create a new `.env` file for your own environment.\n\n## Run Simulator\n\n```bash\n$ python simulator.py \\\n    --env config.math102-lx.env \\\n    --project ~/clineage-simulation/example/example-01 \\\n    --config config.json\n```\n\n## For Developers\n\n### Updating Mutation Transition Table\n\n- Update `om6_ms_only_ac_28x28.csv`.\n- Update and run `prepare.m`.\n- If the matrix size changes, there are some hardcoded number such as 28 in `run_simul.m` and `adjust_ms_mutation_transition_prob.m`.\n\n### To Do\n\n- maybe decouple from clineage to be runnable totally independently.\n- maybe use MATLAB API for 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