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JLSteenwyk · Sep 18, 2024 · 90142c9 · 90142c9
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diff --git a/_sources/usage/index.rst.txt b/_sources/usage/index.rst.txt
@@ -131,7 +131,7 @@ doi: 10.1093/gbe/evw179.
 
 .. code-block:: shell
 
-	phykit aln_len_no_gaps <alignment>
+	phykit aln_len_no_gaps <alignment> [--cpu <cpu>]
 
 Options: |br|
 *<alignment>*: first argument after function name should be an alignment file 
@@ -155,7 +155,7 @@ in the alignment.
 
 .. code-block:: shell
 
-	phykit alignment_recoding <fasta> [-c/--code <code>]
+	phykit alignment_recoding <fasta> [-c/--code <code> --cpu <cpu>]
 
 Codes for which recoding scheme to use: |br|
 **RY-nucleotide** |br|