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We note that the two methods that first predict OMIM terms, which are then mapped to HPO terms performed poorly (see details in the Supplementary material).

Here, I consider split-based supertree methods that first extract the split information of the input trees and subsequently combine this split information into a phylogeny.

Our approach also offers rapid structural annotation for mutations in proteins vis-à-vis methods that first build a 3D model of a sequence followed by mapping of the mutations.

It therefore, appears important to develop methods that first distinguish between insertion and deletion events in the evolutionary history of the sequences in an alignment, and then treat them separately to add distinct signals to the phylogenetic analysis.

It must be distinguished from the traditional per-species recall (Eq. 2) which is also used frequently, but which punishes all methods that first filter proteins.

Thus, methods that first cluster mutations according to their VAF without considering the variance in the VAFs of individual mutations from the observed read counts, including CITUP (Malikic et al., 2015) and LICHeE (Popic et al., 2014), will not recognize differences in clustering between the low and high coverage data.

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In this paper we propose a method that first uses Principal Component Analysis to extract non-stationaries and then minimize the effect of these non-stationaries by covariate shift adaption of the principal components.

In [11, 16], Winken et al. proposed a coding method that first converts a high bit-depth video sequence into a low bit-depth format, which is then encoded by H.264/AVC as the base layer.

We propose a two-step iterative method that first solves the evolution equation by the implicit midpoint rule and then solves the Helmholtz equation using a three-point sixth-order compact scheme.

People living in very cold climates developed various food-freezing techniques long ago, but Clarence Birdseye is credited with inventing the quick-freezing method that first brought us modern frozen food in 1924.

We consider four meta-methods that first apply a NextGenMap and then a more accurate aligner for rejected reads.

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