diff --git a/EukPhylo-QuickStart.md b/EukPhylo-QuickStart.md index 8a749dc..17bba6e 100644 --- a/EukPhylo-QuickStart.md +++ b/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: 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) - * 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) + * 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) (Katzlab 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 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`)