Sentence examples for median branch length from inspiring English sources
For the shortest branches (0.01 substitutions/site), the median branch length overestimate was ~9%.
For the longest branches (1.4 substitutions/site), the median branch length underestimate was ~30% for 1 kb datasets.
Rtrate (mean rate of molecular evolution at the ingroup root node) was estimated by calculating the median branch length from the root to ingroup tips.
Additionally, fixing the tree topology in this analysis did not affect either the median branch length estimate (less than 1% different from the unfixed topology in all cases) or the variance in the estimates.
Other priors for gamma distribution of the rate at root node and the Brownian motion constant describing the rate variation (i.e., the degree of rate autocorrelation along the descending branches of the tree), were derived from the median branch length for each data set as advised by Thorne et al. [ 32].
For both slow and fast data sets the median branch length, divided by the prior of root age resulted in a value between 0.003 and 0.005 depending on the root age prior; therefore for our preferred estimates we utilized a prior of 0.002 ± 0.002 (standard deviation).
We computed the median branch lengths (in substitutions per codon) for these, and they are shown in Figure 5.
We used Tree Annotator [ 21] to summarize the posterior probability distribution of trees using a maximum clade credibility tree (MCCT) with median branch lengths.
The maximum clade credibility (MCC) tree with median branch lengths and a 95%% highest posterior density (HPD) interval on nodes was reconstructed using TreeAnnotator v1.5.4 [ 34].
As before, we partitioned 3′ UTRs into ten conservation bins based upon the median branch-length score (BLS) of the reference-species nucleotides (Friedman et al., 2009).
Despite such a wide range of variability, the median sister branch length ratio is highly robust and shows strong positive correlation with the branch length ratio in the tree of concatenated ribosomal proteins (rS = 0.62 and rS = 0.65, P< 0.0001 for T1 and T2, respectively).
