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updated readme
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sumit-walia committed Nov 11, 2024
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## <a name="construct"></a> PanMAN Construction
Once the package is installed, PanMANs can be constructed from PanGraph [or GFA or MSA] and Tree topology (Newick format) using <i>panmanUtils</i>. Here we provide examples for constructing PanMANs from PanGraph (JSON), users can follow the instructions provided in [wiki](https://turakhia.ucsd.edu/panman/) for other methods.
### Building PanMAN from the provided dataset
Once the package is installed, PanMANs can be constructed from PanGraph [or GFA or MSA] and Tree topology (Newick format) using <i>panmanUtils</i>. Here we provide examples for constructing PanMANs from PanGraph (JSON) and custom dataset. Alternatively, users can follow the instructions provided in [wiki](https://turakhia.ucsd.edu/panman/) for other methods.
### Building PanMAN from PanGraph

**Step 1:** Check if `sars_20.json` and `sars_20.nwk` files exist in `test` directory. Otherwise, follow the instructions to download the dataset.

```bash
cd $PANMAN_HOME/dataset
TODO
```
**Step 1:** Check if `sars_20.json` and `sars_20.nwk` files exist in `test` directory.

**Step 2:** Run <i>panmanUtils</i> with the following command to build a panman from PanGraph:

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