From fcf1763a8ab36a5ed72f632d6c57a74defbc0776 Mon Sep 17 00:00:00 2001
From: MCLeleu <123706003+MCLeleu@users.noreply.github.com>
Date: Tue, 13 Aug 2024 13:17:43 -0400
Subject: [PATCH] Updated PhyloToL Part 2: MSAs, trees, and contamination loop
 (markdown)

---
 ...-2:-MSAs,-trees,-and-contamination-loop.md | 26 +++++++++----------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md b/PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md
index 399df6c..45ef1c1 100644
--- a/PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md
+++ b/PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md
@@ -17,22 +17,22 @@ The code to run PhyloToL Part 2 in full is
 > python Scripts/phylotol.py --start raw --end trees --gf_list  listofOGs.txt --taxon_list taxon_list.txt --data Input_folder --output Output_folder  > Output1.out
 
 Example of listofOGs.txt
->OG6_111062
+OG6_111062
 OG6_105827
->OG6_107533
->OG6_116087
->OG6_105227
+OG6_107533
+OG6_116087
+OG6_105227
 
 Example of taxon_list.txt
->Am_tu_He65
->EE_cr_Gthe
->Pl_gr_Vaul
->Ba_pa_Mlot
->Op_me_Hsap
->Sr_st_Fves
->Sr_ci_Sx06
->Op_fu_Gzea
->Op_me_Lcha
+Am_tu_He65
+EE_cr_Gthe
+Pl_gr_Vaul
+Ba_pa_Mlot
+Op_me_Hsap
+Sr_st_Fves
+Sr_ci_Sx06
+Op_fu_Gzea
+Op_me_Lcha
 
 
 Modularities