Figure 6

Simplification of an ABC gene tree, main example. i) Part of the original ABC gene tree, visualized by the TreeSimplifier GUI. On the very left, an arrow marks mouse ABCc4, which is part of the ABCC4 subtree, first internal repeat ("Mus_musc ABCc4 Pt: 1"; "Pt: 1" denotes the position of the repeat, distinguishing the first and the second "half" in case of ABC proteins [see appendix 1). On the very right, another arrow marks human ABCC10 from the ABCC10 subtree, again of the first internal repeat. In between, a subtree of fly sequences is found, and this subtree also features a gene fragment that is the second domain repeat in the Anopheles sequence ebi1450 (dashed arrow). In the bottom-right, subtrees including sequences from yeast, worm and fly are shown first (small arrow), followed by ABCC7 and the rest of the tree (circle). Subtree labels ("SL") denote the bootstrap value and branchlength associated with internal nodes. ii) Part of the simplified tree automatically provided by TreeSimplifier, and a manual simplification (inset, for comparison, taken from 1). In the automatic simplification, no difference was made between Anopheles gambiae and Drosophila melanogaster. Thus, the ABCC4 subtree follows species phylogeny up to the Coelomata (Vertebrata and fly, see the top-left arrow), and the subtree bottom left in the original tree (triangle arrow) contributes another edge labeled "Fly ABCC Pt: 1". Since different internal repeats (first half versus second half) are not treated as classified consistently in case of ABC proteins, "Pt: 1" and "Pt: 2" cannot be unified (see dashed arrow), although they are glossed over in the manual simplification; "Pt: 2" is most likely a mis-annotation by the RiPE pipeline. The ABCC10 subtree follows species phylogeny, and it is replaced by the single leaf "Fungi_Metazoa ABCC10 Pt. 1" (see the arrow at the very right). There are some more subtrees on the bottom right, namely (Fungi/Metazoa, Bilateria) (small arrow), Fungi/Metazoa and Vertebrata ABCC7. The manual compression (inset) glosses over some fly sequences (triangle arrow) in case of ABCC4, because it treats any mix of Drosophila and Anopheles as a single fly contribution to the gene tree, which is then included, together with Vertebrata ABCC4, in the leaf "Coelomata ABCC4". Moreover, human simplification uses more specific labels such as "Yeast/Worm" instead of "Fungi/Metazoa". TreeSimplifier took much less than a second to derive the entire cartoon tree of 397 leaves.