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Updated QuickStart EukPhylo (markdown)

Adri K. Grow 2025-02-04 10:10:21 -05:00
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QuickStart-EukPhylo.md

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### Modularity of options and replacing the Hook database ### Modularity of options and replacing the Hook database
EukPhylo part 1 for transcriptomes is composed of 7 scripts. User can choose to start or stop at each step by changing the -1 and/or -2 options. EukPhylo part 1 for transcriptomes is composed of 7 scripts. User can choose to start or stop at each step by changing the -1 and/or -2 options.
If a user choose to use their own gene families database, they need to replace the Hook.fasta file in the Database folder, and build a diamond version of their own file; with adjusting the naming system of sequences as the only requirement. If a user chooses to use their own gene family database, they need to replace the Hook.fasta file in the Databases folder and build a diamond version of their own file; with adjusting the naming system of sequences as the only requirement.
To add the XPC option, only available for transcriptomes, user need to add the -x option in their command line. To add the XPC option, only available for transcriptomes, user need to add the -x option in their command line.