diff --git a/Examples/commands/1-Annotate.sh b/Examples/commands/1-Annotate.sh
deleted file mode 100644
index 0cbf1f761f09afee7b9582ff6aa89024d743f211..0000000000000000000000000000000000000000
--- a/Examples/commands/1-Annotate.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-# With prokka
-PanACoTA annotate -d Examples/genomes_init -r Examples/1-res-prokka -l Examples/input_files/list_genomes.lst -n EXAM --l90 3 --nbcont 10
-
-
-# With prodigal
-PanACoTA annotate -d Examples/genomes_init -r Examples/1-res-prodigal -l Examples/input_files/list_genomes.lst -n EXAM  --l90 3 --prodigal --small 
diff --git a/Examples/commands/2-Annotate.sh b/Examples/commands/2-Annotate.sh
new file mode 100644
index 0000000000000000000000000000000000000000..4021c88ec99c02f840c5d6d5c94dedd415137245
--- /dev/null
+++ b/Examples/commands/2-Annotate.sh
@@ -0,0 +1,9 @@
+# Only QC
+PanACoTA annotate -d Examples/genomes_init -l Examples/input_files/list_genomes.lst -r Examples/2-res-QC -Q
+
+# With prokka
+PanACoTA annotate -d Examples/genomes_init -r Examples/2-res-prokka -l Examples/input_files/list_genomes.lst -n GENO --l90 3 --nbcont 10
+
+
+# With prodigal
+PanACoTA annotate -d Examples/genomes_init -r Examples/2-res-prodigal -l Examples/input_files/list_genomes.lst -n GENO  --l90 3 --prodigal --small 
diff --git a/Examples/commands/2-Pangenome.sh b/Examples/commands/2-Pangenome.sh
deleted file mode 100644
index 0342cee5cc4dc3a638fbc81eb5145d03fecb0675..0000000000000000000000000000000000000000
--- a/Examples/commands/2-Pangenome.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-PanACoTA pangenome -l Examples/1-res-Annotate/LSTINFO-list_genomes.lst -n EXAMPLE4 -d Examples/1-res-Annotate/Proteins -i 0.8 -o Examples/2-res-pangenome
-
diff --git a/Examples/commands/3-Corepers.sh b/Examples/commands/3-Corepers.sh
deleted file mode 100644
index d44e764fcd874ec3c12e02ce97a5dcac3400e201..0000000000000000000000000000000000000000
--- a/Examples/commands/3-Corepers.sh
+++ /dev/null
@@ -1 +0,0 @@
-PanACoTA corepers -p Examples/2-res-pangenome/PanGenome-EXAMPLE4.All.prt-clust-0.8-mode1_2019-02-12_13-25-01.tsv.lst
diff --git a/Examples/commands/3-Pangenome.sh b/Examples/commands/3-Pangenome.sh
new file mode 100644
index 0000000000000000000000000000000000000000..7b82819d9c52f958f7a3c97d1c227ae5bf3c8000
--- /dev/null
+++ b/Examples/commands/3-Pangenome.sh
@@ -0,0 +1,2 @@
+PanACoTA pangenome -l Examples/2-res-prokka/LSTINFO-list_genomes.lst -n GENO3 -d Examples/2-res-prokka/Proteins -i 0.8 -o Examples/3-pangenome
+
diff --git a/Examples/commands/4-Align.sh b/Examples/commands/4-Align.sh
deleted file mode 100644
index 1cd6bfc18825adcb94985fac6e06af269f70dd43..0000000000000000000000000000000000000000
--- a/Examples/commands/4-Align.sh
+++ /dev/null
@@ -1 +0,0 @@
-PanACoTA align -c Examples/3-coregenome/PersGenome_PanGenome-EXAMPLE4.All.prt-clust-0.8-mode1_2019-02-12_13-25-01.tsv.lst_1.lst -l Examples/1-res-Annotate/LSTINFO-list_genomes.lst -d Examples/1-res-Annotate/ -o Examples/4-Algn -n EXAMPLE4
diff --git a/Examples/commands/4-Corepers.sh b/Examples/commands/4-Corepers.sh
new file mode 100644
index 0000000000000000000000000000000000000000..e0b42c83f96f1806ebf0e5364910da40ea59c8fe
--- /dev/null
+++ b/Examples/commands/4-Corepers.sh
@@ -0,0 +1,5 @@
+# core genome
+PanACoTA corepers -p Examples/3-pangenome/PanGenome-GENO3.All.prt-clust-0.8-mode1_<date>.tsv.lst -o Examples/4-corepers
+
+# strict persistent at 95%
+PanACoTA corepers -p Examples/3-pangenome/PanGenome-GENO3.All.prt-clust-0.8-mode1_<date>.tsv.lst -o Examples/4-corepers -t 0.95
diff --git a/Examples/commands/5-Corepers.sh b/Examples/commands/5-Corepers.sh
new file mode 100644
index 0000000000000000000000000000000000000000..81eb407d93173093bef0ff5f489cac0d336e564b
--- /dev/null
+++ b/Examples/commands/5-Corepers.sh
@@ -0,0 +1 @@
+PanACoTA align -c Examples/4-corepers/PersGenome_<pangenome-filename>_1.lst -l Examples/2-res-prokka/LSTINFO-list_genomes.lst -n GENO3_1 -d Examples/2-res-prokka -o Examples/5-align
diff --git a/Examples/commands/5-Tree.sh b/Examples/commands/5-Tree.sh
deleted file mode 100644
index f5e8cdbbf4fbf05a74225a6789bbe2c56fd72145..0000000000000000000000000000000000000000
--- a/Examples/commands/5-Tree.sh
+++ /dev/null
@@ -1 +0,0 @@
-PanACoTA tree -a Examples/4-Algn/Phylo-EXAMPLE4/EXAMPLE4.grp.aln
diff --git a/Examples/commands/6-Tree.sh b/Examples/commands/6-Tree.sh
new file mode 100644
index 0000000000000000000000000000000000000000..db0770316a7feaadf19d50d6b7a3563ea42dc696
--- /dev/null
+++ b/Examples/commands/6-Tree.sh
@@ -0,0 +1 @@
+PanACoTA tree -a Examples/5-align/Phylo-GENO3_1/GENO3_1.grp.aln -o Examples/6-tree
\ No newline at end of file