diff --git a/QuickStart-EukPhylo.md b/QuickStart-EukPhylo.md index 96e7990..0ce4b44 100644 --- a/QuickStart-EukPhylo.md +++ b/QuickStart-EukPhylo.md @@ -109,8 +109,8 @@ If a user choose to use their own gene families database, they need to replace t # EukPhylo part 2 = MSA - Trees - Contamination Removal - Concatenation -## Set Up: -### Structure: +## EPp2: +### Set up: * 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) * 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