From d5a90de21522f73b3cb226a9359b2da97320b728 Mon Sep 17 00:00:00 2001 From: Katzlab Date: Thu, 13 Feb 2025 15:31:06 -0500 Subject: [PATCH] Updated EukPhylo Part 2: MSAs, trees, and contamination loop (markdown) --- EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md b/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md index b496dbc..0478692 100644 --- a/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md +++ b/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md @@ -9,7 +9,7 @@ EukPhylo part 2 starts from the “ReadyToGo” files produced by part 1 (or any Example output files for EukPhylo part 2 and the contamination loop can be found [here](https://doi.org/10.6084/m9.figshare.26662018.v1). -# Set Up +# Install (only need to do once) ## Dependencies The following are required to run EukPhylo part 1. The dependencies are confirmed to work using the version numbers in parentheses, though other versions may work as well. @@ -24,6 +24,8 @@ The following are required to run EukPhylo part 1. The dependencies are confirme * [MAFFT](https://mafft.cbrc.jp/alignment/software/) (version 7.49) * [IQ-Tree](http://www.iqtree.org/) (version 2.1.2) and/OR [RAxML](https://cme.h-its.org/exelixis/web/software/raxml/) (version 8.2.12) and/OR [FastTree](https://microbesonline.org/fasttree/) (version 2.1) +# Setup + ## Input data and folder structure Running EukPhylo Part 2 requires at least four items in your main directory: @@ -31,6 +33,8 @@ Running EukPhylo Part 2 requires at least four items in your main directory: * A folder containing your input files * A taxon list * An OG list +* An Output folder +* a shell script (or equivalent) to load modules and run programs ++ See below for details.