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Table 1 TAD callers analyzed in this study

From: Comparison of computational methods for the identification of topologically associating domains

TAD caller Approach # parameters Hierarchical domains Inter-TAD gaps
3DNetMod Network features 18 Overlapping Yes
armatus Linear score 1 Overlapping No
arrowhead Linear score 1 Overlapping Yes
CaTCH Linear score 0 Nested No
CHDF Clustering 2 Disjoint No
chromoR Linear score 2 Disjoint No
ClusterTAD Clustering 2 Disjoint No
Directionality Index (DI) Linear score 3 Disjoint Yes
EAST Linear score 0 Disjoint Yes
GMAP Linear score 0 Nested Yes
HiCExplorer Linear score 5 Disjoint Yes
HiCseg Statistical model 3 Disjoint No
HiTAD Linear score 0 Disjoint Yes
ICFinder Clustering 2 Disjoint No
Insulation Score (IS) Linear score 5 Disjoint Yes
matryoshka Linear score 1 Nested Yes
MrTADFinder Network features 1 Disjoint No
PSYCHIC Statistical model 1 Nested No
spectral Network features 2 Disjoint No
TADbit Statistical model 0 Disjoint No
TADtree Statistical model 6 Overlapping No
TopDom Linear score 1 Disjoint Yes