HGT Inference via Tree Comparison

<p>Raw difference between the SD and the MAST metrics for a given pair of trees tends to increase when HGT is involved in one tree. For example, the raw SD and MAST scores for Gene Tree 1 and the W-G tree are 2 and 2, respectively, while the SD and MAST scores for Gene Tree 2 and the W-G tree are 8 and 2, respectively. This difference between the SD and the MAST scores indicates possible HGT in Gene Tree 2; the (c and d) clade are transferred to the g lineage (dotted arrow). In Gene Tree 1, the (c and d) clade cannot be inferred as transfers because many other factors could have caused the local uncertainty in branching, which should be presented in polytomous form.