File: README.md

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# PMEN1 dataset
The PMEN1 dataset (12 Mbyte multi-FASTA alignment file) which was used in the paper was downloaded from:
```
https://figshare.com/ndownloader/files/33468725
```
and was run through gubbins with all of the default parameters:
```
gunzip PMEN1.aln.gz
run_gubbins.py --prefix PMEN1 --first-tree-builder rapidnj --first-model JC --tree-builder raxmlng --model GTR PMEN1.aln
```
This directory contains the output files generated. The analysis took ~20 seconds to run. When rendered in Phandango, the output resembles:

![PMEN1 analysis](PMEN1_output.png)