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Updated EukPhylo QuickStart (markdown)

Adri K. Grow 2025-02-17 14:34:04 -05:00
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EukPhylo-QuickStart.md

@ -112,7 +112,7 @@ If a user choose to use their own gene families database, they need to replace t
### Set up: ### Set up:
In a main project directory: In a main project directory:
* Create a `Scripts` folder containing the 8 scripts from GitHub [here](https://github.com/Katzlab/EukPhylo/tree/main/PTL2/Scripts) * Create a `Scripts` folder containing the 8 scripts from GitHub [here](https://github.com/Katzlab/EukPhylo/tree/main/PTL2/Scripts)
* In addition to the scripts, also add the `trimal-trimAl` and `guidance.v2.02` folders, as downloaded from [here](https://github.com/inab/trimal) and [here](https://github.com/anzaika/guidance) (Smith College HPC (Grid) users see [here](https://docs.google.com/document/d/1tDxaCrVEHckyvlaaY58lNQnJ4UHTRAMICdR7xzzjPTE/edit?tab=t.0)) * In addition to the scripts, also add the `trimal-trimAl` and `guidance.v2.02` folders, as downloaded from [here](https://github.com/inab/trimal) and [here](https://github.com/anzaika/guidance). Smith College HPC (Grid) users see [here](https://docs.google.com/document/d/1tDxaCrVEHckyvlaaY58lNQnJ4UHTRAMICdR7xzzjPTE/edit?tab=t.0)
* Create an empty output folder (e.g. `Output`) for results (i.e. guidance and tree outputs) * Create an empty output folder (e.g. `Output`) for results (i.e. guidance and tree outputs)
* Create a list of ten-digit codes for your target and outgroup taxa (e.g. `taxa.txt`) * Create a list of ten-digit codes for your target and outgroup taxa (e.g. `taxa.txt`)
* Create a folder (e.g. `R2Gs`) that contains the AA ReadyToGo fasta files for all taxa (from `taxa.txt`) * Create a folder (e.g. `R2Gs`) that contains the AA ReadyToGo fasta files for all taxa (from `taxa.txt`)