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In this manner, DT created an interactive branching topology in which the branch taken at each intersection is determined by a rule related to a MD of the molecule, and lastly, each terminating leaf of the tree is assigned to a particular category, i.e., A (active) or B (inactive) [27 30].
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In Voevodsky's motivic homotopy theory, familiar classical geometry was replaced by homotopy theory — a branch of topology in which a line may shrink all the way down to a point.
The optimal gene trees produced by Bayesian and ML searches showed nearly identical topology, in which the tip branches within species were short, and species were separated by much longer branches (Figure 3).
The better-supported protein phylogenies favor a topology in which neo- and parabodonids branch as the deepest and next-deepest branches of the Metakinetoplastina (i.e. all kinetoplastids except the clade to which P. amoebae belongs), and their common ancestor is therefore also the ancestor of eubodonids and trypanosomatids (Fig. 3).
However, the original chloroplast topology was not significantly better than the topology in which F. densistipulata was branched with other Cyathistipulae taxa to make this subsection monophyletic.
For Segment 1, all four methods produce a single congruent topology (topologies in which major branch points are in identical relative positions are considered congruent).
When two lineages fail to coalesce on the earliest branch in which they can coalesce, this can result in a gene tree having a different topology than the species tree.
Further error is contributed by uncertainty in the phylogeny itself, both in the branching topology and the branch length estimates [ 31].
In such cases, the load imposed by the adsorption forces is unevenly distributed over different structural elements of the molecular architecture according to the branching topology.
For partitioned analyses all parameters, including branch-length rate multipliers, were unlinked across partitions; the only exceptions were branch lengths and topology, which were linked.
The BI posterior probability of each topology was calculated by integrating over all eight branch length sets for that topology, using a prior distribution in which the probability of each topology and each branch length set on that topology matched the true generating conditions.
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