parameters.md

@@ -122,7 +122,7 @@ BiG-SCAPE Classes that should NOT be included in the classification. E.g. "`--ba
 --cutoffs {0.0-1.0}
 ```
 
-Generate networks using multiple raw distance cutoff values, example: `--cutoffs 0.1, 0.25, 0.5, 1.0`. Default: all values from 0.10 to 0.80 with 0.05 intervals. For every cutoff value, a different network file will be generated. Regarding the interactive visualization, only the highest cutoff will be shown. Automatic clustering of Gene Cluster Families will be done using each cutoff.
+Generate networks using multiple raw distance cutoff values, example: `--cutoffs 0.1, 0.25, 0.5, 1.0`. Default: `c=0.3`. For every cutoff value, a different network file will be generated. Regarding the interactive visualization, only the highest cutoff will be shown. Automatic clustering of Gene Cluster Families will be done using each cutoff.
 
 ## Clans
 
@@ -130,31 +130,31 @@ Generate networks using multiple raw distance cutoff values, example: `--cutoffs
 --clans-off
 ```
 
-By default BiG-SCAPE will perform a second layer of clustering and attempt to group GCFs. Toggle to disactivate
+By default, BiG-SCAPE will perform a second layer of clustering to group GCFs into GCCs. Toggle to deactivate this.
 
 ```
---clan_cutoff {0.0-1.0} {0.0-1.0}
+--clans_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: 0.3). 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`)
-                        
+Cutoff Parameters for which clustering families into clans will be performed in raw distance. First value is the cutoff used for finding GCFs that will be used for Clan calling (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). Average distance between members of each pair of GCFs are used as inter-GCF distance. Every pair of GCFs linked with a distance of `GCC cutoff value` or less will be taken into account. Example: `--clan_cutoff 0.5 0.8`)
+
 Learn more about [GCFs and GCCs](GCFs and GCCs).
 
 ## Hybrids
 
 ```
---hybrids
+--hybrids-off
 ```
 
-Toggle to also add BGCs with hybrid predicted products from the PKS/NRPS Hybrids and Others classes to each subclass (e.g. a 'terpene-nrps' BGC will will usually be classified in Others would be added to the Terpene and NRPS classes)
+By default, BGCs with hybrid predicted products from the PKS/NRPS Hybrids and Others classes will be included into each subclass (e.g. a `terpene-nrps` BGC that will usually be classified in Others would be added to both the Terpene and NRPS classes). This means that the same cluster may appear in different classes. Toggle to deactivate
 
 ## Alignment Mode
 
 ```
---mode {global,lcs,auto}
+--mode {global,glocal,auto}
 ```
 
-Alignment mode for each pair of gene clusters. 'global' (default) the whole list of domains of each BGC are compared; 'lcs': Longest Common Subcluster mode. Redefine the subset of the domains used to calculate distance by trying to find the longest slice of common domain content per gene in both BGCs, then expand each slice. 'auto' use LCS when at least one of the BGCs in each pair has the 'contig_edge' annotation from antiSMASH v4+, otherwise use global mode on that pair. Learn more about the alignment modes [here](alignment)
+Alignment mode used when comparing each pair of gene clusters. `global`: the whole list of domains of each BGC are compared; `glocal` (default): Longest Common Subcluster mode. In it, the subset of the domains used to calculate distance is redefined by finding the longest slice of common domain content per gene in both BGCs, then expands each slice. `auto`: use glocal mode when at least one of the BGCs in each pair has the `contig_edge` annotation from antiSMASH v4+, otherwise use global mode on that pair. Learn more about the alignment modes [here](alignment)
                         
 ## Anchorfile
 
@@ -186,7 +186,7 @@ Skip multiple alignment of domains' sequences. Use if alignments have been gener
 --mibig
 ```
 
-Use included BGCs from the [MIBiG database](https://mibig.secondarymetabolites.org/). Currently, version 1.3 of the database is included in the BiG-SCAPE project (about 1,400 BGCs) as a compressed file, which will be unzipped the first time the `--mibig` option is used.
+Use included BGCs from the [MIBiG database](https://mibig.secondarymetabolites.org/). Currently, version 1.3 of the database is included in the BiG-SCAPE project (about 1,400 BGCs) as a compressed file, which will be unzipped the first time the `--mibig` option is 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 and correspond to the files found in each entries' page)
 
 ## Query BGC mode