Input formats of primetv. (a) The host tree, S, and (b) the guest tree, G, in Newick format. (c) The leaf map between the host tree in (a) and the guest tree in (b) in tabular form. In each row, the left column has a guest tree leaf name and the right column has the associated host tree leaf name. (d, e, f) The reconciliation γ can be input to primetv in three different formats: (d) The full reconciliation, γ, in tabular format. For a host tree node x (the left column), γ(x) (the right column of the same row) comprise all guest tree vertices whose incoming edges appear on the incoming edge of x in the reconciled tree, cf. γ(4) as indicated in Figure 3(a). Notice that a guest vertex can map to several host vertices. (e) The reduced reconciliation, , in tabular format. This is achieved from a full reconciliation, γ, by, for each host tree vertex x, removing from γ(x) all guest vertices that are ancestral to other vertices in γ(x), e.g., 8 in γ(4). (f) The reconciled tree (G, γ) in PrIME format. This is a Newick tree with PrIME tags added to tree vertices; a sequence of PrIME tags are always given within brackets and are preceded by the tag specifier &&PRIME. For a guest vertex, v, the tag ID indicates a unique number identifying v. If no ID-tag is given, e.g., in Newick format, identity numbers are assigned automatically. The tag AC indicates the ID-numbers of the host tree vertices that v maps to in the reduced reconciliation ; these host tree vertices should always form a path in the host tree. Additionally, for a leaf l, the tag S indicate the label of the host tree leaf that l maps to. When reading host trees primetv will assume that numbers after colons (:) represent (ultrametric) edge times rather than edge lengths. This can be made explicit by using the tag ET in the PrIME format.
Sennblad et al. BMC Bioinformatics 2007 8:148 doi:10.1186/1471-2105-8-148