SuperCRUNCH - 4a - Cluster Blast

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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. A majority of the total markers were included for this style of similarity searching. The other markers (mtDNA, SACS, both portions of RAG1) used the reference based similarity searching (not shown here). The file sets were manually moved to the respective input folders. ``` python Cluster_Blast_Extract.py -i /Path/To/4a-Cluster-BLAST/input -o /Path/To/4a-Cluster-BLAST/output -b dc-megablast --max_hits 200 -m span --threads 4 ```

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