Complete documentation on how to run SuperCRUNCH is available at: https://github.com/dportik/SuperCRUNCH/wiki
The following generalized commands were used to run the analysis. Please note that the `/Path/To/` should be changed to the actual file locations.
This analysis was used to produce a concatenated alignment of all markers. Note that the AHE markers are included here too. The main SuperCRUNCH analysis steps were focused on generating the Legacy and NPCL marker sets.
```
python Concatenation.py -i /Path/To/12-Concatenate/input -o /Path/To/12-Concatenate/output --informat fasta --outformat phylip -s dash
```
The output on screen looked like this:
```
Found 307 fasta files to concatenate.
Found 5,326 unique taxa across alignment files.
Gathering sequences for all taxa (this could take some time)...
Done.
Writing partitions file.
Writing concatenated alignment.
Total alignment length = 381,201 bp.
Total number of sequences included = 90,196.
--------------------------------------------------------------------------------------
Finished. Total elapsed time: 0:00:25.818981 (H:M:S)
--------------------------------------------------------------------------------------
```
