Therefore, we apply KInfer to the network model we inferred with the time-lagged correlation based inference procedure described in the previous section.
In the proposed method, the networks are inferred with a priori determined maximum time lag r and a threshold θ.
The tree was inferred with FastTree v1.4 under the general time reversible model and a gamma correction for variable evolutionary rates with eight classes.
Inferring such systems is a considerable statistical challenge and it has recently been shown that some parameters cannot be inferred with any degree of certainty from time-course data.
Topology of the strict consensus tree was inferred with Bayesian methods, using a general time-reversible model with gamma distributed rate variation, and topological results were congruent with previous studies (Klak et al., 2003b; Fig. 2).
Based on 179 Alu insertions, a robust phylogenetic hypothesis has been constructed and the placement for Miopithecus is inferred with statistically significant support for the first time.
In general, the ancestral effective size N A and the time of onset of growth τ were inferred with some certainty.
Marginal posterior densities for population split times and split proportions could not be inferred with accuracy [24].
(b) ML tree inferred with selected sequences.
By applying a Bayesian coalescent analysis to 212 serially sampled partial N sequences (1,275-bp 1,275-bperred the time scale of RABV evolution in lineages associated weth vampinferred.
