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Updated QuickStart EukPhylo (markdown)

Adri K. Grow 2025-01-28 14:46:23 -05:00
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QuickStart-EukPhylo.md

@ -110,7 +110,8 @@ If a user choose to use their own gene families database, they need to replace t
## Set Up: ## Set Up:
* A folder called “Scripts” containing all the [scripts from Github](https://github.com/Katzlab/EukPhylo/tree/main/PTL2/Scripts) ### Structure:
* A folder called “Scripts” with scripts from [here](https://github.com/Katzlab/EukPhylo/tree/main/PTL2/Scripts) on Github
* Inside the Scripts folder, you also need to add the trimal-trimAl and guidance.v2.02 folders, as downloaded from [here](http://trimal.cgenomics.org/downloads) and [here](https://github.com/anzaika/guidance) * Inside the Scripts folder, you also need to add the trimal-trimAl and guidance.v2.02 folders, as downloaded from [here](http://trimal.cgenomics.org/downloads) and [here](https://github.com/anzaika/guidance)
* An empty output folder named as you wish for all output files (which will include trees and guidance files when done running), for example: Output_folder * An empty output folder named as you wish for all output files (which will include trees and guidance files when done running), for example: Output_folder
* A folder called “OutgroupR2Gs” containing the amino acid (AA) ReadyToGo fasta files for your target and outgroup taxa listed in your taxon_list.txt * A folder called “OutgroupR2Gs” containing the amino acid (AA) ReadyToGo fasta files for your target and outgroup taxa listed in your taxon_list.txt