Next: , Previous: , Up: Descriptive   [Contents] Number of sequence clusters.

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.