Figure 1

Prunier algorithm: example of a Prunier run. Example of reconciliation of an unrooted gene tree T _G with a rooted species tree T _S by searching for the maximum statistical agreement forest (MSAF). In the gene tree, blue branches are those common to the two trees whereas red branches indicate conflicting edges, i.e., those found in T _G but not in T _S . Support values are shown for conflicting edges. In this example, two rounds are needed to reconcile the two trees. The agreement function "Agree" corresponds here to the "fast" version of Prunier: a gene (sub-)tree is considered in statistical agreement with the species (sub-)tree if no conflicting edge above 80 exists. At each round, clades corresponding to common edges (blue branches) are ranked by decreasing scores. This score reflects the conflict (combination of the support values) removed when the edge is cut (symbolized by "Rm{clade}"). The highest scoring subtree candidate to transfer is removed if it is in agreement with the species tree. The output of Prunier is a statistical agreement forest (SAF), composed of a reconciled backbone subtree (non-transferred sequences: {ABFGHIK}) and as many reconciled subtrees (transferred sequences) as lateral gene transfers (LGT). In this example, two LGT events are inferred: {J} and {CDE} have been transferred.