diff --git a/PTL2/run_phylotol.sh b/PTL2/run_phylotol.sh
deleted file mode 100644
index e9e0bb6..0000000
--- a/PTL2/run_phylotol.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/bin/bash
-#SBATCH --job-name=YOUR_PROJECT_NAME ##change this to a shortened name of your project
-#SBATCH --output=Run_phylotol.%j.out # Stdout (%j expands to jobId)
-#SBATCH --nodes=1
-#SBATCH --ntasks=1
-#SBATCH --ntasks-per-node=4 ##change to number of srun when running multiple instances
-#SBATCH --mem=150G
-#SBATCH --mail-type=ALL
-#SBATCH --mail-user=email@smith.edu ##add your email address
-
-module purge       #Cleans up any loaded modules
-
-module use /gridapps/modules/all    #make sure module locations is loaded
-
-module load slurm
-module load ETE
-module load Biopython
-module load DIAMOND/0.9.30-GCC-8.3.0
-module load MAFFT
-module load BioPerl
-module load RAxML
-module load IQ-TREE/2.1.2-foss-2020a
-export PATH=$PATH:/beegfs/fast/katzlab/grid_phylotol_setup/programs/standard-RAxML-master
-
-parent='/beegfs/fast/katzlab/<fill in with your path>/' #do not edit this line before katzlab/, add your path starting with the name of your folder
-
-#if you are running batches, you need an srun line for each batch!
-srun -D ${parent} python3 ${parent}Scripts/phylotol.py --start raw --end trees --gf_list listofOGs.txt --taxon_list taxon_list.txt --data OutgroupR2Gs --output ${parent}Output_folder > Output_folder.out &
-#srun -D ${parent} python3 ${parent}Scripts/phylotol.py --start raw --end trees --gf_list mei_batch2.txt --taxon_list taxon_list.txt --data OutgroupR2Gs --output ${parent}mei_output2 > mei_output2.out &
-#srun -D ${parent} python3 ${parent}Scripts/phylotol.py --start raw --end trees --gf_list mei_batch3.txt --taxon_list taxon_list.txt --data OutgroupR2Gs --output ${parent}mei_output3 > mei_output3.out &
-#srun -D ${parent} python3 ${parent}Scripts/phylotol.py --start raw --end trees --gf_list mei_batch4.txt --taxon_list taxon_list.txt --data OutgroupR2Gs --output ${parent}mei_output4 > mei_output4.out &
-
-wait