parameters.md

@@ -196,6 +196,14 @@ Use included BGCs from the [MIBiG database](https://mibig.secondarymetabolites.o
 
 Instead of making an all-VS-all comparison of all the input BGCs, choose one BGC to compare with the rest of the set (one-VS-all). The query BGC does not have to be within inputdir. The distances that will be used for the GCF and GCC analysis are all that are equal or lower than the maximum cutoff value. This will only take into account the BiG-SCAPE class(es) that the Query BGC belongs to.
 
+## Domain whitelist
+
+```
+--domain_whitelist
+```
+
+Only include BGCs which include domains with the Pfam accessions found in the domain_whitelist.txt file. In this file, each line contains a single Pfam accession (with an optional comment, separated by a tab). Lines starting with "#" are ignored. See the file for an example using the P450 domain.
+
 ## Version
 
 ```