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Reliable prior information about branch lengths and other model parameters is seldom available in practice, so virtually all analyses have used "uninformative" diffuse prior distributions (such as branch length priors uniform from 0 to 5 or exponential with mean 0.1, which are offered as the default values in common software packages).
First, one could sample a larger number of genes, which would then provide increased information about branch lengths through the opportunity to observe more incongruence in gene trees.
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Trajectories of large objects like blood vessels can be tracked with high precision and provide important information about branching patterns of vessels in tumor genesis and metastasis formation.
PIC's transform character states at tips to incorporate information about branching.
However, we believe that the main reason for the disparity is that Gage and Freckleton [ 33] used a very poorly resolved phylogeny that included 12 "soft" polytomies" (i.e., polytomies not due to true simultaneous speciation events but to lack of information about branching pattern) encompassing 57 out of the 83 (69%) species in their study.
Visual comparison of tree topologies is qualitative only, and information about absolute branch lengths is disregarded.
Nevertheless, we believe that information about composition, branch architecture and sequences of the CEA glycan moieties should be sufficient to improve the specificity of CEA to allow its use as a colon tumor marker.
Second, PhyloCSF also takes advantage of genome-wide training data to provide prior information about the branch lengths in the phylogenetic tree and the codon frequencies, rather than attempting to reestimate these a priori in each individual alignment.
Qualitative information about the branching structures could be readily obtained from linear viscoelasticity, non-linear oscillatory shear experiments and strain hardening in elongational experiments.
Qualitative information about the branching structures could be readily obtained from linear viscoelasticity, nonlinear oscillatory shear experiments and strain hardening in elongational experiments.
However, this technique failed to provide structural information about the branching pattern of and types of covalent bonds within the various GPI glycoforms of VSG.
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