parameters.md

@@ -6,7 +6,7 @@ Type `python bigscape.py -h` to display a list of all available parameters. See
 
 ## help
 
-Type `-h` or `--help` to display all available options
+Type `-h` or `--help` to display all current available options
 
 ## Label
 
@@ -106,7 +106,7 @@ By default, BiG-SCAPE separates the analysis according to the BGC product and wi
 --no_classify
 ```
 
-By default, BiG-SCAPE classifies the output files analysis based on the BGC product. Toggle to                        deactivate (note that if the `--mix` parameter is not activated, BiG-SCAPE will not create any network file but all intermetiate files will be processed)
+By default, BiG-SCAPE classifies the output files analysis based on the BGC product. Toggle to deactivate (note that if the `--mix` parameter is not activated, BiG-SCAPE will not create any network file but all intermetiate files will be processed)
 
 ## Filter classes
 
@@ -127,16 +127,16 @@ Generate networks using multiple raw distance cutoff values, example: `--cutoffs
 ## Clans
 
 ```
---clans
+--clans-off
 ```
 
-If activated, BiG-SCAPE will perform a second layer of clustering and attempt to group GCFs assigned from clustering
+By default BiG-SCAPE will perform a second layer of clustering and attempt to group GCFs. Toggle to disactivate
 
 ```
---clan_cutoff {0.0-1.0}
+--clan_cutoff {0.0-1.0} {0.0-1.0}
 ```
 
-Cutoff Parameters for which clustering families into clans will be performed in raw distance. First value is the GCF cutoff value used in clan clustering (default: 0.5). If this GCF cutoff value is not included within `--cutoffs`, it will be added automatically. Second value is the GCC cutoff value for clustering families into clans (default: 0.8). Average linkage for BGCs in a family is used for distances between families, so, every pair of GCFs linked with an average distance of GCC cutoff value or less will be taken into account. Example: `--clan_cutoff 0.5 0.8`)
+Cutoff Parameters for which clustering families into clans will be performed in raw distance. First value is the GCF cutoff value used in clan clustering (default: 0.3). If this GCF cutoff value is not included within `--cutoffs`, it will be added automatically. Second value is the GCC cutoff value for clustering families into clans (default: 0.7). Example: `--clan_cutoff 0.5 0.8`)
                         
 Learn more about [GCFs and GCCs](GCFs and GCCs).