Table 2: Phylogenetic states of all components at all identified progression markers for the data of Navin et al. [14]. Columns show the states for the six inferred components (C1–C6). The additional normal component (C0) used to root the tree is included for completeness. “1” corresponds to an amplified region and “0” to nonamplified.

Marker ID C0 C1 C2 C3 C4 C5 C6

1 0 1 0 1 1 1 0
2 0 1 0 1 1 1 0
3 0 0 0 1 0 0 0
4 0 0 0 1 0 0 0
5 0 0 0 1 1 1 0
6 0 0 0 0 1 0 1
7 0 0 0 0 1 0 1
8 0 0 0 1 0 0 0
9 0 1 0 1 0 1 0
10 0 1 0 1 1 1 0
11 0 1 0 1 1 1 0
12 0 1 0 1 1 1 0
13 0 0 0 0 1 1 0
14 0 0 1 0 1 0 0
15 0 0 0 0 0 0 1
16 0 1 0 0 1 0 0
17 0 0 0 0 1 0 0
18 0 0 0 0 1 0 1
19 0 0 0 0 1 1 1
20 0 0 0 0 1 1 1
21 0 0 0 0 1 1 1
22 0 0 1 0 0 0 0
23 0 0 1 0 0 0 0
24 0 1 0 0 0 0 1
25 0 0 0 1 1 1 0
26 0 0 0 1 1 1 0
27 0 0 0 1 1 1 0