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Fig. 3 | BMC Bioinformatics

Fig. 3

From: A phylogenetic approach for weighting genetic sequences

Fig. 3

Computational demand of different approaches to character frequency estimation. Violin plots summarise the running times, in seconds, of different methods. All analyses were run on a MacBook Pro 2017. Each plot contains values for 10 replicates of the scenario of the unscaled tree in Fig. 1 and nucleotide data. Time cost for computing frequencies from un-weigthed observed characters is not shown as it is negligible. Time demand of Bayesian variants of PNS weights is also not shown, as it is the same as for their non-Bayesian variants (Bayesian variants only require the addition of pseudocounts compared to non-Bayesian variants). ‘FastTree’ represents the cost of running phylogenetic inference with FastTree prior to weight calculation. Orange violin plots show the total cost (including computational cost of phylogenetic inference for methods requiring a phylogeny). Blue violin plots show the cost of calculating the scores without taking into account the cost of phylogenetic tree inference. For \(w^D_s\) and ‘PhyML’, blue and orange plots overlap. Calculating HH94 weights is, overall, the fastest approach among those considered here, as it does not require phylogenetic inference

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