Fig. 5.
a A phylogenetic tree with 11 present sequences. A single alignment column with a high degree of identity across sequences indicate evolutionary conservation. b A phylogenetic tree can easily be converted to a factor graph, here shown for a phylogenetic tree with only 3 species. Note that the common ancestors are typically not available for sequencing and their sequences are unknown. The internal variables are therefore unshaded indicating a hidden variable. c The distribution of the conditional expectation of the number of substitutions over the whole phylogenetic tree, given the present sequences. The distribution is obtained by simulating 105 times. d We use IS to estimate the tail of the distribution by sampling n=1,000 scores. Two different α-values were used: 0, corresponding to naive sampling and 1.5. Note that naive sampling has much wider confidence bands in the tail compared to importance sampling