From 2b9a887c043e039764906eb2ab40c78576edbb62 Mon Sep 17 00:00:00 2001
From: MCLeleu <123706003+MCLeleu@users.noreply.github.com>
Date: Wed, 14 Aug 2024 10:33:21 -0400
Subject: [PATCH] Create run_phylotol_command_line.txt

Example command line to run PhyloToL
---
 .../Running_PTLp2/run_phylotol_command_line.txt             | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 PTL2/Examplar_runs/Running_PTLp2/run_phylotol_command_line.txt

diff --git a/PTL2/Examplar_runs/Running_PTLp2/run_phylotol_command_line.txt b/PTL2/Examplar_runs/Running_PTLp2/run_phylotol_command_line.txt
new file mode 100644
index 0000000..217a0b2
--- /dev/null
+++ b/PTL2/Examplar_runs/Running_PTLp2/run_phylotol_command_line.txt
@@ -0,0 +1,6 @@
+### Download and make your own ReadyToGo_AA_GC3_labelled folder with ReadyToGo files
+### Update the taxa list with the taxa files in your ReadyToGo folder
+### Download the Script folder
+### than run :
+
+python3 Scripts/phylotol.py --start raw --end trees --gf_list list_ogs.txt --taxon_list taxa_list.txt --data ReadyToGo_AA_GC3_labelled --output Output --similarity_filter --sim_cutoff 0.95 --og_identifier OG6 --tree_method iqtree > log1.out