Sequence analysis. The intracellular regions of Notch ligands from different organisms were aligned automatically using ClustalW (score matrix: Gonnet, penalty for gap opening, 10; penalty for gap closing, 1; penalty for gap extension, 0.2; penalty for gap separation, 8). The cladogram was generated using the neighbor joining algorithm and drawn using Mega . Confidence values for grouping in the tree were obtained by bootstrapping (N = 1000) and normalized to 100. Identified groups are labelled as J1, J2, D1, D4, D3, and colored accordingly. The branching points between J1 and J2 and between D1 and D4 groups are also labeled. Ligands sharing the same architecture in the extracellular regions are enclosed in brackets. Similar results were obtained using T-Coffee  and MUSCLE .