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In contrast, the advantage of MR is that input trees can be unrooted and that the area around the optimum is searched for equally scoring trees.
PRICE implemented three techniques for detecting such sequences: (1) alignment to a user-provided database of repetitive element sequences; (2) alignment to a similar database generated by PRICE during assembly based on regions of anomalously high read coverage; and (3) equally scoring alignments to multiple distinct initial contigs.
This slows down the last part of the PluMiST algorithm, because equally scoring trees are explored by NNI.
Where Phenomizer reports many equally scoring values, the differential diagnosis is performed using several different but overlapping term sets, for example with a key feature being listed as mandatory rather than observed, or with removal of clinical features that are felt to likely represent a second, unrelated disorder.
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This demonstrates the effect of equally scored candidates on ranking results.
The expected ranks, which partially account for equally scored candidates as calculated in [16], are shown in the lower part of the table.
The information elicited from the user consists of a pairwise comparison between the requirements that are ordered differently in equally scored prioritization.
The expected top ranks calculated as in Allen et al. [16], which handles ties of equally scored candidates in a uniformly random manner, are also given when comparing the two in silico fragmenters.
All edges in the graph were equally scored (score = 1).
In our case, we simply sort the equally scored genes alphabetically and assign the ranks.
All 5 new GO terms were equally scored and represent mitochondrion (GO 0005739), seed germination (GO 0009845), seedling development (GO 0090351), Group III intron splicing (GO 0000374) and vegetative to reproductive phase transition of meristem (GO 0010228).
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