T1 is an input tree built on four taxa a1, a2, a3and a4. The internal nodes of T1 are labeled as x0, x1 and x2. S1 is the only seed obtained from T1 when k = 2 and c = 0. That is S1 is identical to the clade rooted at x2. S1, S2 and S3 are the seeds extracted from T1 when k = 2 and c = 1. They are all extracted from the clade rooted at x1 by contracting a3, a2 and a1 respectively.
Ramu et al. BMC Bioinformatics 2012 13:256 doi:10.1186/1471-2105-13-256