added deduplication to manual

man/pages/usage.md

@@ -480,3 +480,17 @@ Output files:
 | `--unalign_input` | Generates a copy of the input alignment with no gaps | False |
 | `--unalign_output` | Generates a copy of the output alignment with no gaps | False |
 
+#### Removing Duplicates
+
+This function removes sequences with duplicate names from the alignment, keeping the first (by default) or last (if specified) instance of the name, rather than failing if duplicated names are present.
+
+Output files:
+
+* **`OUTFILE_STEM_cleaned.fasta`** - the cleaned output file generated by CIAlign will have the duplicates removed
+
+| Parameter | Description | Default |
+| ------------------------------------------------------ |------------------------------------------------------------------------------------------------------------- | ------------ |
+| `--deduplicate_ids` | Remove sequences with duplicate names from the input. | False |
+| `--duporder` | Set to `first` to keep the first instance of the sequence name and `last` to keep the last | first |
+
+