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For clustering methods requiring a similarity matrix as input, we used the Pearson's correlation in our initial evaluation.
Variation in prokaryote composition among biotopes was assessed with Principal Coordinates Analysis (PCO) using the cmdscale function in R with the Bray Curtis distance matrix as input.
Based on term document frequency matrix as input PLSA finds phishing and non-phishing topics using tempered expectation maximization.
The models use the trip matrix as input and split the matrix into separated matrices, one for each mode.
PHAT only takes a boundary matrix as input, so it is not possible to conduct a direct comparison of it with the other implementations.
For a query sequence, we generate the position specific scoring matrix as input features by searching against SWISS-PROT database using the PSI-BLAST tool.
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However, as FFT requires rectangular matrices as input, we sampled, via linear interpolation, a constant number of points along the contour with respect to time.
Kaur et al. [15], [16] further enhanced the performance of β-turn prediction by use of secondary structure predictions and evolutionary information in form of position specific scoring matrices as input to the neural networks (BetaTPred2 method) [17].
We transformed total abundance data into 0/1 matrices as input into the program EstimateS [48] to compute rarefaction curves, non-parametric richness estimators and several indices of alpha diversity.
We used these matrices as input for MDS.
Network inference was performed using the tool NetGenerator V2.0, employing two separate data matrices as input.
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