CountClusters counts the number of sequence clusters. This requires that a clustering tree was previously computed (see below).
maf.filter= \ [...], SequenceStatistics( \ statistics=(\ \ [...], CountClusters( \ tree=bionj, \ threshold=0.001), \ [...]), \ ref_species=species1, \ file=data.statistics.csv), \ [...]
The tag name used to store the previously computed tree.
The threshold to use in order to compute clusters. A threshold of 0.001 for instance means that sequences within each cluster will be divergent by maximum 0.001, while sequences in distinct clusters will be divergent by at least 0.001.