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The source condition is constrained using a vulcanian explosion model by Fagents and Wilson (1993).
The continuous Galerkin approximation is constrained using a flux-corrected transport (FCT) algorithm.
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In the same way DNA was modeled, the tertiary structure of RNA is constrained using an elastic network.
The map was constrained using a voxel-level minimum statistic threshold and a cluster size threshold.
Binning was constrained using a minimum threshold on percent identity for alignments that met the default maximum E-value.
The internal relationships of durocryptodires were constrained using a molecular topology [ 79] (i.e., (Emydidae (Geoemydidae + Testudinidae)) + (Chelonioidea (Chelydridae + Kinosternoidea))).
All hydrogen-containing bonds were constrained using a recent implementation (Lippert et al., 2007) of the M-SHAKE algorithm (Krautler et al., 2001).
The root node ages of our trees were constrained using a uniform prior with an upper bound of 75 mya based on recent MRCA age estimates of Cyprinidae [ 43].
To simulate more difficult alignment cases where the candidate sequence is distant to the closest match in the reference MSA, reference sequence selection may be constrained using a maximum identity parameter.
Following Fine et al. [ 18] and De Nova et al. [ 17], the age of the MRCA of all Burseraceae (Node D) was constrained using a secondary calibration to place a normally distributed prior age with a mean of 64.92 Ma and a standard deviation of 2.35.
In [ 13], the following mixture of prior is proposed: (5) p (a i j ) = (1 - π i j ) δ 0 (a i j ) + π i j N (a i j | 0, 1 ), where π ij is the probability of a nonzero a ij and δ0 is the Dirac delta function at 0. Meanwhile, A is constrained using the lower triangular method.
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