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.
There are files in the SuperCRUNCH - 2 - Starting Materials section used here (https://osf.io/zrbvm/).
This analysis selected representative sequences per species, per marker. We identified some problematic sequences and so used an exclusion list. I ran this analysis for 16S, 12S, and the remaining markers indpendently to achieve the desired outcome.
12S:
```
python Filter_Seqs_and_Species.py -i /Path/To/5-Sequence-Selection/input-12S -o /Path/To/5-Sequence-Selection/output -s oneseq -f length -m 300 -t /Path/To/Starting-Materials/Taxon-List-Anura-July_2_2022-no-outgroups.txt --accessions_include /Path/To/Starting-Materials/SeqSelection-Accessions-Include.txt --accessions_exclude /Path/To/Starting-Materials/SeqSelection-Accessions-Exclude-12S.txt > SeqSelection-12S.log
```
16S:
```
python Filter_Seqs_and_Species.py -i /Path/To/5-Sequence-Selection/input-16S -o /Path/To/5-Sequence-Selection/output -f length -s oneseq -m 300 -t /Path/To/Starting-Materials/Taxon-List-Anura-July_2_2022-no-outgroups.txt --accessions_include /Path/To/Starting-Materials/SeqSelection-Accessions-Include.txt --accessions_exclude /Path/To/Starting-Materials/SeqSelection-Accessions-Exclude.txt > SeqSelection-16S.log
```
Other markers:
```
python Filter_Seqs_and_Species.py -i /Path/To/5-Sequence-Selection/input-other -o /Path/To/5-Sequence-Selection/output -s oneseq -f length -m 300 -t /Path/To/Starting-Materials/Taxon-List-Anura-July_2_2022-outgroups.txt --accessions_include /Path/To/Starting-Materials/SeqSelection-Accessions-Include.txt --accessions_exclude /Path/To/Starting-Materials/SeqSelection-Accessions-Exclude.txt > SeqSelection-All.log
```
