From a8e7a1d33659a00e6c9998f16d262f375329fa38 Mon Sep 17 00:00:00 2001
From: GiuliaRibeiro <41350697+GiuliaRibeiro@users.noreply.github.com>
Date: Fri, 18 Apr 2025 13:17:23 -0400
Subject: [PATCH] Updated EukPhylo Part 2: MSAs, trees, and contamination loop
 (markdown)

---
 EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md b/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md
index 0b021f9..2edd835 100644
--- a/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md
+++ b/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md
@@ -141,6 +141,8 @@ Argument | Default | Choices | Description
 -- | -- | -- | --
 --tree_method | iqtree_fast | iqtree, iqtree_fast, raxml, fasttree | Program to use for tree-building.
 
+NOTE: These processes are resource-intensive. Each system has its own syntax and requirements for running resource-intensive jobs. Here, we added examples of how we run in our local Smith College 'grid' system and on the more powerful HPC Unity cluster. Please adjust the 'tree.py' and 'run_eukphylo.sh' scripts to match with your system's capabilities, as specified in the scripts. 
+
 ## Contamination loop
 
 The contamination coop (CL) is implemented within EukPhylo to allow the removal of contaminants based on the topology of each tree (phylogeny-informed contamination removal). Three modes are available: sister-, subsister-, and clade-based contamination removal. All modes take a user defined file of 'rules,' used to identify the sequences to remove. We first provide an overview of the three modes and then give details on running below.