diff --git a/Examples/commands/5-Align.sh b/Examples/commands/5-Align.sh
index ea710648091ebf2ae224c7b5f9c0e595ef33bf21..69c7886d8416e2ee017b9f4a3d7e6d2790842bda 100644
--- a/Examples/commands/5-Align.sh
+++ b/Examples/commands/5-Align.sh
@@ -2,4 +2,4 @@
 PanACoTA align -c Examples/4-corepers/PersGenome_PanGenome-GENO3.All.prt-clust-0.8-mode1.lst-all_1.lst -l Examples/2-res-prokka/LSTINFO-list_genomes.lst -n GENO3_1 -d Examples/2-res-prokka -o Examples/5-align
 
 # only run align step of example
-PanACoTA align -c Examples/input_files/align-input/coregenome-example.lst -l Examples/input_files/pan-input/LSTINFO-list_genomes.lst -n GENO3_1 -d Examples/input_files/pan-input -o Examples/5-align
\ No newline at end of file
+PanACoTA align -c Examples/input_files/align-input/coregenome-example.lst -l Examples/input_files/pan-input/LSTINFO-list_genomes.lst -n GENO3_1 -d Examples/input_files/pan-input -o Examples/5-align-alone