--- /dev/null
+#!/bin/bash
+
+echo ""
+echo "Setting executable flag for Clustalw..."
+chmod +x clustalw/src/clustalw2
+
+echo "Setting executable flag for Clustal Omega..."
+chmod +x clustalo/src/clustalo
+
+echo "Setting executable flag for Mafft..."
+chmod +x mafft/binaries/*
+chmod +x mafft/scripts/*
+
+echo "Setting executable flag for Mafft dependency fasta34 ..."
+chmod +x fasta34/fasta34
+
+echo "Setting executable flag for Muscle..."
+chmod +x muscle/muscle
+
+echo "Setting executable flag for Probcons..."
+chmod +x probcons/probcons
+
+echo "Setting executable flag for T-Coffee..."
+chmod +x tcoffee/t_coffee_source/t_coffee
+
+echo "Setting executable flag for DisEMBL..."
+chmod +x disembl/disembl disembl/sav_gol disembl/DisEMBL.py
+
+echo "Setting executable flag for GlobPlot..."
+chmod +x globplot/GlobPlot.py globplot/sav_gol
+
+echo "Setting executable flag for IUPred..."
+chmod +x iupred/iupred