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Example sentences for: topologies

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For all three possible unrooted tree topologies maximum-likelihood values and posterior probabilities were calculated using in-house JAVA programs that were written utilizing classes from the Phylogenetic Analysis Library version 1.0 [ 54 ] and parts of Vanilla package version 1.0 [ 54 ] . If not indicated otherwise, likelihood values were estimated using the automatically selected suitable substitution model (chosen from BLOSUM62, CPREV, Dayhoff, JTT, MTREV24, VT and WAG) with no ASRV.
While pairwise sequence identity is not a universally dependable measure of phylogenetic information content, these values illustrates that the sequences within a QuartOP are neither identical to one another, nor so divergent as to be saturated with substitutions and of questionable homology [ 30 ] . Using only the most conserved QuartOPs does not change the qualitative result: each of the three possible tree topologies is supported by about an equal number of QuartOPs (see supplementary material).
The topologies differed in the placement of Stilnolepis , which was placed outside of Subtribe Artemisiinae by MP and at the base of the subtribe by both ML and Bayes.
Further, the predicted trans-membrane topologies of HNOB domain proteins suggest an intracellular localization for all occurrences of this domain.
In both cases the varieties were grouped into clusters such that the topologies of the trees were broadly similar for some of the clusters of varieties.