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Branches were collapsed if maximum branch length was zero.
Branch length was scaled by the maximum branch length to range from 0 to 1.
As proposed by Posada & Crandall [ 53] this haplotype should represent the most ancestral one, whereas the most derived ones are related to it with a maximum branch length of twelve mutational steps (H55 and H52).
A newly sequenced strain (Sahul64) isolated from Australian Aboriginals [ 40] has a draft genome available and incorporation of this genome in phylogenetic analysis shows maximum branch length in its clade representing the higher evolutionary time.
Branch length was scaled by the maximum branch length to range from 0 to 1. (B ) Lag, (C ) Late Log (LL), (D ) Diauxic Shift (DS), (E ) Post Shift (PS), (F ) Plateau (PLAT).
Σ should be scaled to a height of one instead of being scaled to tree maximum branch length, because units of branch length may be meaningful for the phylogeny (e.g. millions of years, number of mutations...) but they are not related to the units of the trait data, and so relative lengths should be used.
Similar(54)
In summary, both fixed- and unfixed-parameter results suggest that error in model parameter estimation contributes to maximum likelihood branch length misestimation in some simple simulations.
A more sophisticated weighting scheme uses "expected branch lengths", i.e. the product of the posterior likelihood and the maximum likelihood branch length of the interior edge of the corresponding quartet tree.
Similarly the F-box subclade has a shorter maximum-likelihood branch length than the other subclade.
The first subclade within the clade I contains sequences only from angiosperm plants and the average maximum-likelihood branch length is shorter than that of the other subclade, which contains mostly sequences from mosses.
Since the last common ancestor and as depicted on the distance matrices and highlighted by boxplots of maximum-likelihood branch length distributions (Technical Appendix 2 Figure 3), there are more mutations fixed in the VP1 region than in the 3CD region, and more in the 3CD region than in 5′-UTR, which is indicative of a variable rate of evolution in these regions.
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