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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. This analysis ensured that all protein-coding markers were adjusted to the correct reading frame. This prepared them for alignment with the translation alignment method MACSE. The nuclear and mtDNA markers were analyzed separately, using the correct translation table. ``` python Coding_Translation_Tests.py -i /Path/To/8-Adjust-ORF/input-nucdna -o /Path/To/8-Adjust-ORF/output-nucdna --table standard > translation-nuc.log ``` ``` python Coding_Translation_Tests.py -i /Path/To/8-Adjust-ORF/input-mtdna -o /Path/To/8-Adjust-ORF/output-mtdna --table vertmtdna > translation-mtdna.log ```
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