From ab05c14c759c1f11b9b4b84dade89f4a56bf85b9 Mon Sep 17 00:00:00 2001
From: MCLeleu <123706003+MCLeleu@users.noreply.github.com>
Date: Tue, 13 Aug 2024 12:27:13 -0400
Subject: [PATCH] Updated PhyloToL Part 2: MSAs, trees, and contamination loop
 (markdown)

---
 ...-2:-MSAs,-trees,-and-contamination-loop.md | 21 ++++++++++++++++++-
 1 file changed, 20 insertions(+), 1 deletion(-)

diff --git a/PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md b/PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md
index 364deca..5a27a4e 100644
--- a/PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md
+++ b/PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md
@@ -11,11 +11,30 @@ For those users interested in eukaryotic phylogeny, we provide a database of 1,0
 
 # Running PhyloToL Part 2
 
-Running PhyloToL Part 2 requires at least 4 items in your main directory: 1) A folder named [Scripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL2/Scripts) and containing all scripts from PhyloToL part 2 (**TBD - link to Github?), 2) a folder containing your input files, 3) a taxon list (**TBD - provide example below?) and 4) an OG list (**TBD - provide example below?). Given that PhyloToL part 2 is highly modular and flexible, you will want to be sure of what point to the process of PTLp2 you wish to start and end (**TBD - point to figshare file here -- some figure). The default script starts with raw data and produces trees using scripts 1 - TBD. 
+Running PhyloToL Part 2 requires at least 4 items in your main directory: 1) A folder named [Scripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL2/Scripts) and containing all scripts from PhyloToL part 2, 2) a folder containing your input files, 3) a taxon list and 4) an OG list. Given that PhyloToL part 2 is highly modular and flexible, you will want to be sure of what point to the process of PTLp2 you wish to start and end (**TBD - point to figshare file here -- some figure). The default script starts with raw data and produces trees using scripts 1 - TBD. 
 
 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_105827
+>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
+
+
 Modularities
 * If you want to produce trees, you will keep the default '--end’ parameter set to 'trees' 
 * If you want to produce up to pre-guidance files, you will change the default '--end’ parameter to 'unaligned'