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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), \
[...]
|
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.