From dd51f2188510b69a7cacf574e8fe25fa38512e82 Mon Sep 17 00:00:00 2001
From: MCLeleu <123706003+MCLeleu@users.noreply.github.com>
Date: Wed, 14 Aug 2024 10:36:09 -0400
Subject: [PATCH] Create run_phylotol_command_line.txt

---
 .../Running_CLoop/CladeGrabbing/run_phylotol_command_line.txt | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100644 PTL2/Examplar_runs/Running_CLoop/CladeGrabbing/run_phylotol_command_line.txt

diff --git a/PTL2/Examplar_runs/Running_CLoop/CladeGrabbing/run_phylotol_command_line.txt b/PTL2/Examplar_runs/Running_CLoop/CladeGrabbing/run_phylotol_command_line.txt
new file mode 100644
index 0000000..1533bb4
--- /dev/null
+++ b/PTL2/Examplar_runs/Running_CLoop/CladeGrabbing/run_phylotol_command_line.txt
@@ -0,0 +1,4 @@
+### Download the Script folder
+### than run :
+
+python3 Scripts/phylotol.py --start trees --end trees --data Input --output Output/ --contamination_loop clade --clade_grabbing_rules_file clade_grabbing_rules.txt --clade_grabbing_exceptions exceptions.txt --cl_tree_method iqtree_fast --nloops 1 > log1.out