diff --git a/docs/userguide.rst b/docs/userguide.rst
index 32b15bc2b562da6625576577336473efeb34e70d..412b28a6be2617936c1142d851ab94033074774d 100644
--- a/docs/userguide.rst
+++ b/docs/userguide.rst
@@ -194,7 +194,7 @@ Let's define two enzymes. The first is called 'afterP' (id 28) and cleaves after
 
 .. code-block:: none
 
-    $ rpg -i PKPKPKPK -e 28 29
+    $ rpg -s PKPKPKPK -e 28 29
     >Input_0_afterP_1_1_115.13198_5.54
     P
     >Input_1_afterP_3_2_243.30608_9.4
@@ -214,7 +214,7 @@ Digesting 'PKPKPKPK' using those two enzymes in concurrent mode gives the follow
 
 .. code-block:: none
 
-    $ rpg -i PKPKPKPK -e 28 29 -d c
+    $ rpg -s PKPKPKPK -e 28 29 -d c
     >Input_0_afterP-afterK_1_1_115.13198_5.54
     P
     >Input_1_afterP-afterK_2_1_146.18938_9.4
@@ -248,7 +248,7 @@ For example, using:
 
 .. code-block:: none
 
-    rpg -i QWSDORESDF -e 1 2 3 -m 1.4 2.6
+    rpg -s QWSDORESDF -e 1 2 3 -m 1.4 2.6
 
 will assign a miscleavage probability of `1.4%` to enzyme `1`, a miscleavage probability of `2.6%` to enzyme `2` and a miscleavage probability of `0%` to enzyme `3` (default behavior). For enzyme `1`, each cleavage will then have a probability of 0.014 to **not** occur.
 
@@ -317,7 +317,7 @@ With default verbosity level (no **-v** nor **-q** option), the output is:
 
 .. code-block:: none
 
-    $ rpg -i QWSDORESDF -e 1
+    $ rpg -s QWSDORESDF -e 1
     >Input_0_Asp-N_3_3_419.43738_5.54
     QWS
     >Input_1_Asp-N_8_5_742.78688_4.16
@@ -329,7 +329,7 @@ Increasing verbosity by one, *i.e.* using **-v**, adds information about used op
 
 .. code-block:: none
 
-    $ rpg -i QWSDORESDF -e 1 -v
+    $ rpg -s QWSDORESDF -e 1 -v
     Warning: File 'peptides.fasta' already exit!
     Overwrite it? (y/n)
     y
@@ -349,7 +349,7 @@ Increasing verbosity by two, *i.e.* using **-vv**, also adds statistics about ea
 
 .. code-block:: none
 
-    $ rpg -i QWSDORESDF -e 1 -vv
+    $ rpg -s QWSDORESDF -e 1 -vv
     Warning: File 'peptides.fasta' already exit!
     Overwrite it? (y/n)
     y
@@ -378,7 +378,7 @@ Decreasing verbosity, *i.e.* using **-q** option, removes all information but er
 
 .. code-block:: none
 
-    $ rpg -i QWSDORESDF -e 1 -q 
+    $ rpg -s QWSDORESDF -e 1 -q 
     Warning: File 'peptides.fasta' already exit!
     Overwrite it? (y/n)
     y
@@ -443,13 +443,13 @@ Note that this enzyme will only cleave if it finds the motif C*BAD, where * coul
     Add another enzyme? (y/n)
     n
 
-    $ rpg -i CWBADE -e 43
+    $ rpg -s CWBADE -e 43
     >Input_0_rpg_example_userguide_3_3_307.36728_5.46
     CWB
     >Input_1_rpg_example_userguide_6_3_333.29818_3.4
     ADE
 
-    $ rpg -i FAD -e 43
+    $ rpg -s FAD -e 43
     >Input_0_rpg_example_userguide_0_3_351.35928_3.6
     FAD
 
@@ -482,19 +482,19 @@ It is important to note that for each enzyme, it is enough that one of the rule
     Add another enzyme? (y/n)
     n
 
-    $ rpg -i CWBADE -e 43
+    $ rpg -s CWBADE -e 43
     >Input_0_rpg_example_userguide_3_3_307.36728_5.46
     CWB
     >Input_1_rpg_example_userguide_6_3_333.29818_3.4
     ADE
 
-    $ rpg -i FAD -e 43
+    $ rpg -s FAD -e 43
     >Input_0_rpg_example_userguide_1_1_165.19188_5.54
     F
     >Input_1_rpg_example_userguide_3_2_204.18268_3.6
     AD
 
-    $ rpg -i BAD -e 43
+    $ rpg -s BAD -e 43
     >Input_0_rpg_example_userguide_0_3_204.18268_3.6
     BAD
 
@@ -576,13 +576,13 @@ This enzyme will always cleave before A when not followed by P:
     Add another enzyme? (y/n)
     n
     
-    rpg -i CWBADE -e 43
+    rpg -s CWBADE -e 43
     >Input_0_rpg_example_userguide_3_3_307.36728_5.46
     CWB
     >Input_1_rpg_example_userguide_6_3_333.29818_3.4
     ADE
     
-    rpg -i CWBAPE -e 43
+    rpg -s CWBAPE -e 43
     >Input_0_rpg_example_userguide_0_6_604.67828_3.6
     CWBAPE
 
@@ -616,25 +616,25 @@ This enzyme will always cleave before A (`P1'` ) when not followed by P (`P2'` )
     Add another enzyme? (y/n)
     n
     
-    rpg -i CWBADE -e 43
+    rpg -s CWBADE -e 43
     >Input_0_rpg_example_userguide_3_3_307.36728_5.46
     CWB
     >Input_1_rpg_example_userguide_6_3_333.29818_3.4
     ADE
     
-    rpg -i CWBAPE -e 43
+    rpg -s CWBAPE -e 43
     >Input_0_rpg_example_userguide_0_6_604.67828_3.6
     CWBAPE
     
-    rpg -i GTBAMF -e 43
+    rpg -s GTBAMF -e 43
     >Input_0_rpg_example_userguide_0_6_525.62028_5.54
     GTBAMF
 
-    rpg -i GTBAPE -e 43
+    rpg -s GTBAPE -e 43
     >Input_0_rpg_example_userguide_0_6_473.48328_3.6
     GTBAPE
     
-    rpg -i GTBAME -e 43
+    rpg -s GTBAME -e 43
     >Input_0_rpg_example_userguide_3_3_176.17228_5.54
     GTB
     >Input_1_rpg_example_userguide_6_3_349.40218_3.6