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The refined tree classified biopsies on the basis of gains/losses in seven chromosomes and one chromosomal rearrangement.
As expected, Algorithm MinNADref always yielded a refined tree with a lower or equal number of NADs than the tree given by Algorithm MinDLref, but always had a higher or equal DL-cost.
Of the 107 renal cortical neoplasm biopsies for which a FISH-based classification was obtained (bp-FISH), the optimum concordance achieved using the refined tree was 79% (84/107, Table 3).
We employ a postprocessing procedure to score the resulting trees, but as this potentially involves refining trees to binary trees, it has a worst case run time that is exponential in the number of leaves of the resulting trees (although the score for a single refined tree can be computed by the algorithm M ULTIB UILD in polynomial time).
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The only previously identified gene-specific driver changes in our patients were the HER2 amplifications in patient 6 and two missense mutations in PIK3CA in patients 1, 3, 4, and 5. Our highly refined trees provide an opportunity to ask about their origins relative to the cellular ancestors that our trees have identified.
To test whether such information could be used to refine tree biomass estimates, each monitor was asked to assess wood hardness using a simple classification: "1" for very light wood, "2" for floater (light wood) and "3" for sinker (heavy wood).
The entire process of refining trees into smooth, lightweight paper comes at a high energy cost and produces serious carbon dioxide emissions (that contribute to global climate change).
If Q is an embedded subtree of T, the tree T(A) is called the embedding of Q in T. We say that tree Q is refined by tree T (or that T refines Q) if the set of clusters of Q is a subset of the set of clusters of T| A; i.e., T| A is a refinement of Q.
The new algorithm is consistently faster than the O(n d) time algorithm for the r8s (with edge contraction) simulated trees and for the Buneman and refined Buneman trees.
SuperFine uses a two-step technique, where the first step produces a typically unresolved tree called the "Strict Consensus Merger" (SCM) tree, and the second step then refines this tree.
Tóth, A. et al. Iteratively refined guide trees help improving alignment and phylogenetic inference in the mushroom family bolbitiaceae.
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