Comparison of groupings according to eBGs versus groupings by other algorithms.

Note: Bootstrap is an abbreviation for the Gene by Gene Bootstrap approach with 50% support. 1092 distinct STs were tested by all three methods. BAPS with an upper bound of 400 assigned all STs to 216 clusters. The two other methods identified singletons (ClonalFrame, 189) or excluded individual STs whose branches did not receive 50% support (Bootstrap, 569), which were excluded from further comparisons. No. eBGs per cluster shows the numbers of clusters that contained 0, 1, 2,…7. eBGs according to each of the three methods. Clusters per eBG indicates the number of clusters identified by each of the three methods to which any STs within an eBG were assigned. Maximal number of clusters per eBG: BAPS, 2; ClonalFrame, 2; Bootstrap, 4. The significance of these associations was tested by 10,000 permutations of assignments of STs to eBGs for each of the three clustering assignments or by 10,000 permutations of the clustering assignments for the real eBG assignments of STs. None of the 10,000 permutations exceeded the number of eBGs found per cluster or the number of eBGs assigned to one cluster except that 9.5% of the permutations of the number of eBGs per BAPs cluster equalled or exceeded 71.