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2.3.1.12 Number of sequence clusters.

CountClusters counts the number of sequence clusters. This requires that a clustering tree was previously computed (see below).

Synopsis:

maf.filter=                                 \
    [...],                                   
    SequenceStatistics(                     \
        statistics=(\                       \
            [...],                                                    
            CountClusters(                  \
                tree=bionj,                 \
                threshold=0.001),           \
            [...]),                         \
        ref_species=species1,               \
        file=data.statistics.csv),          \
    [...]

Arguments:

tree={string}

The tag name used to store the previously computed tree.

threshold={double}

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.