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 style of similarity searching requires reference sequences. They are provided here but can also be found in the SuperCRUNCH reference sequence sets (https://github.com/dportik/SuperCRUNCH). The markers analyzed here include all mtDNA markers, SACS, and both portions of RAG1. The other nuclear markers used the automated similarity searching (not shown here). The file sets were manually moved to the respective input folders. I ran this analysis in two parts, splitting the markers between each analysis. The commands below show the general usage. The required reference files and keys are included in the inputs folder in this module. ``` python Reference_Blast_Extract.py -i /Path/To/4b-Reference-BLAST/12S-CO1-ND1-ND2-ND4 -o /Path/To/4b-Reference-BLAST/output --multisearch /Path/To/4b-Reference-BLAST/multisearch-12S-CO1-ND1-ND2-ND4.txt -b dc-megablast --max_hits 100 -m span --threads 4 ``` ``` python Reference_Blast_Extract.py -i /Path/To/4b-Reference-BLAST/16S-CYTB-RAG1-SACS -o /Path/To/4b-Reference-BLAST/output --multisearch /Path/To/4b-Reference-BLAST/multisearch-16S-CYTB-RAG1-SACS.txt -b dc-megablast --max_hits 100 -m span --threads 4 ```