The genomic fluidity between two genomes is defined as the number of unique gene
families divided by the total number of gene families (Kislyuk et al, 2011). This is averaged
over n.sim random pairs of genomes to obtain a population estimate.
The genomic fluidity between two genomes describes their degree of overlap with respect to gene
cluster content. If the fluidity is 0.0, the two genomes contain identical gene clusters. If it
is 1.0 the two genomes are non-overlapping. The difference between a Jaccard distance (see
distJaccard
) and genomic fluidity is small, they both measure overlap between
genomes, but fluidity is computed for the population by averaging over many pairs, while Jaccard
distances are computed for every pair. Note that only presence/absence of gene clusters are
considered, not multiple occurrences.
The input pan.matrix is typically constructed by panMatrix
.