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Added more documentation authored by Jorge Navarro Muñoz's avatar Jorge Navarro Muñoz
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......@@ -14,7 +14,7 @@ BiG-SCAPE tries to (recursively) read BGC information stored as GenBank files fr
BiG-SCAPE then uses the [Pfam database](http://pfam.xfam.org/) and `hmmscan` from the HMMER (v3.1b2) suite to [predict Pfam domains](domain_prediction) in each sequence.
For every pair of BGCs in the set(s), the pairwise distance between this BGCs is calculated as the weighted combination of the [Jaccard](distance#jaccard), [AI](distance#ai) and [DSS](distance#dss) indices. Two types of output are generated: text files which include [Network files](output#network_files) and an [Interactive visualization](output#interactive_visualization). This is done taking into account different cutoff values for the distances (i.e. only pairs with Raw Distance < `cutoff` are written in the final `.network` file).
For every pair of BGCs in the set, the pairwise distance between this BGCs is calculated as the weighted combination of the [Jaccard](distance#jaccard), [AI](distance#ai) and [DSS](distance#dss) indices. Two types of output are generated: text files which include [Network files](output#network_files) and an [Interactive visualization](output#interactive_visualization). This is done taking into account different cutoff values for the distances (i.e. only pairs with Raw Distance < `cutoff` are written in the final `.network` file).
The distances for each cutoff value will be used to try to [automatically define](GCFs and GCCs) 'Gene Cluster Families' (GCFs) and 'Gene Cluster Clans' (GCCs).
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