parameters.md

@@ -213,10 +213,13 @@ Skip multiple alignment of domains' sequences. Use if alignments have been gener
 ## MIBiG
 
 ```
---mibig, --mibig13
+--mibig, --mibig14, --mibig13
 ```
 
-Use included BGCs from the [MIBiG database](https://mibig.secondarymetabolites.org/). Currently, versions 1.4 (`--mibig`) and 1.3 (`--mibig13`) of the database are included in the BiG-SCAPE project as a compressed file, which will be unzipped the first time the `--mibig` or `--mibig13` option are used. (Note that this set is different from the bundle found in the downloads section of the MIBiG site; these GenBank files have been processed by antiSMASH to annotate the BGC type; they correspond to the files found in each entries' pages)
+Use included BGCs from the [MIBiG database](https://mibig.secondarymetabolites.org/). Currently, versions 2.1 (`--mibig`), 1.4 (`--mibig14`) and 1.3 (`--mibig13`) of the database are included in the BiG-SCAPE project as a compressed file, which will be unzipped the first time these options are used. 
+
+Note that this sets are different from the bundle found in the downloads section of the MIBiG site; these GenBank files have been processed by antiSMASH to annotate the BGC type. Additionally, the latest version is an unofficial version of the current content of MIBiG 'repository' page (i.e. it contains a few more BGCs than the official 2.0 bundle)
+
 
 ## Query BGC mode
 
@@ -226,13 +229,13 @@ 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 includelist
 
 ```
---domain_whitelist
+--domain_includelist
 ```
 
-Only include BGCs which include (any) 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. Pfam accessions are case-sensitive.
+Only include BGCs which include (any) domains with the Pfam accessions found in the `domain_includelist.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. Pfam accessions are case-sensitive.
 
 ## Version