From ac9fbffae5ae35c1eaf736fd76c5b1b6be4ffd28 Mon Sep 17 00:00:00 2001 From: MCLeleu <123706003+MCLeleu@users.noreply.github.com> Date: Tue, 13 Aug 2024 12:23:58 -0400 Subject: [PATCH] Updated PhyloToL Part 2: MSAs, trees, and contamination loop (markdown) --- PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md | 2 +- 1 file changed, 1 insertion(+), 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 78c1d62..364deca 100644 --- a/PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md +++ b/PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md @@ -11,7 +11,7 @@ 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 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 (**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. 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