Summary Tree from Posterior Samples: Supplemental Information

We examined ve methods for selecting the of the summary tree topology, MCC, TCB, CCD, HPF and HPV. The rst four are explained in the article, and the last is simply picking the topology of the tree with the highest posterior value. The article shows results for only for MCC and TCB, and here we show why. Table 1 and 2 summarise the pairwise performance of the ve methods. Each method can be coupled with one of the 7 ways of assigning branch lengths, RBS,SRBS,HSO,RAS,MED,CAT, and AVG. For each test case there are 7 pairing: for example, when comparing MCC and TCB we have MED,TCB Vs. MED,MCC, RBS,TCB Vs. RBS,MCC, HSO,TCB Vs. HSO,MCC and so on. For each pairing there are 8 error measure. Table 1 shows the percentage of cases where method X was signi cantly better than Y, computed over the all pairings, error measures and 4000 bootstrap trials.