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The time-scaled phylogenetic tree on the third dataset was reconstructed by using the Bayesian Markov Chain Monte Carlo approach implementing the evolutionary model selected by ModelTest, setting the evolutionary rate to the value previously estimated and the best fitting models (so as for the clock and the demographic model) were selected using a Bayes factor (BF, using marginal likelihoods).
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This simulation framework is combined with single-pass reliability analysis approach to implement the evolutionary algorithm.
Maximum likelihood trees were calculated in PhyML [43] using the online tool DIVER (http://indra.mullins.microbiol.washington.edu/cgi-bin/DIVER/diver.cgi), which implemented the evolutionary model GTR+I+G for all subjects.
When a reserve is implemented, the evolutionary response of this population is almost indistinguishable from that of a migratory population with a feeding-ground reserve.
The mutation score is used only in the work of Henard et al. (2014), which implements the (1+1) Evolutionary Algorithm (EA) algorithm, and considers the operators defined in (Henard et al. 2013a).
In the experimental part of the paper, we compare the performance of an evolutionary algorithm (implementing the two Cayley-encodings considered) in several OTNDP instances: first, we test the proposed techniques in randomly generated instances, and second, we tackle a real application of the OTNDP: the optimal design of an interactive voice response system (IVR) in a call center.
According to informants, designing and implementing the initiative has been an evolutionary and organic process.
We consider the reconstruction of signals from nonuniformly spaced samples using a projection onto convex sets (POCSs) implemented with the evolutionary time-frequency transform.
Alignments for individual gene families supporting variations of the WAG model (with addition of rates across sites variation and empirically estimated base frequencies) were concatenated, and phylogeny was determined using RAxML (Stamatakis 2006) implementing the WAG + GAMMA + F evolutionary model (Reeves 1992; Yang 1993; Whelan and Goldman 2001).
Phylogenetic trees were reconstructed using PhyML (Guindon and Gascuel 2003) implementing the WAG + I + GAMMA evolutionary model (Reeves 1992; Yang 1993; Whelan and Goldman 2001), collecting five bootstrap samples for the bootstrap amalgamation procedure linked to gene-tree species-tree reconciliation.
To solve the challenge of consistency, two different models can be adopted to implement the SDRAN architecture: "evolutionary" and "clean slate".
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