Sentence examples for branches within the tree from inspiring English sources
Numbers at nodes (>50%) indicate support for the internal branches within the tree obtained by bootstrap analysis (percentages of 100 bootstraps).
Bootstrap resampling [ 70] was undertaken using ML, NJ and MP with 1000 bootstrap replicates in order to assign support to particular branches within the tree.
Most of these groups are clades (terminal branches) within the tree, but others are merely close to some more basal node.
Confidence levels for individual branches within the tree were checked for each algorithm by repeating the PHYLIP analysis with 1000 bootstraps [ 32] using the SEQBOOT program in the PHYLIP package.
Since minicollagens are encoded by short and fast evolving sequences, most branches within the tree are not well-supported (Maximum likelihood [ML] bootstrap percentage BP < 50%, Bayesian posterior probability PP < 0.7), precluding reconstruction of the order of the duplication events.
We consider a protein to be of eukaryotic origin when it has no homologs in prokaryotes, or when the prokaryotic branches within the tree are mono-phyletic as in Figure 1a.
The resulting tree is shown in Figure 3. Surprisingly, we found that all eleven Physcomitrella hexokinases are more closely related to each other than to other plant hexokinases, thus forming a single branch within the tree.
This is driven by the model's attempt to locate the incommensurate sequence patterns (0, 1, 0, 0, 1) and (0, 0, 0, 1, 1) as arising from mutations on the same branch within the tree.
Thus, the P450ome size does not appear to have undergone expansion for around 6 hundred to 7 hundred Million years in the Ascomycete branch within the tree of life [ 25].
From the 1-ratio model the dN/dS for each branch within the tree was estimated at 0.08, and the dN/dS ratio of the subtree was estimated at 0.06.
Prolines are proposed to play an important structural role in peptaibols by creating a kink in the peptaibol chain, and Clade 3 occupies a long branch within the tree, suggesting it is highly diverged from the other A-domains (Additional file 2).
