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15 changes: 15 additions & 0 deletions doco/Running_DecentTree.md
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<h1>Running decenttree</h1>

This is an example of how to run decenttree with Neighbor Joining algorithm. Other algorithms can be found in https://github.com/iqtree/decenttree/blob/master/doco/Algorithms.md.

If the input file is in multiple sequence alignment format (.fasta, can be compressed)

```
decentTree -fasta $inputFile -t NJ -out $outputFile
```

If the input file is in distance matrix format

```
decentTree -in $inputFile -t NJ -out $outputFile
```

<h2>Command-line options</h2>

| Option | Argument | Description |
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