Sentence examples for used to simulate alignments from inspiring English sources

Posterior samples of gene trees, for both simulated and real alignments, were downloaded together with the 'true' gene trees used to simulate alignments from the dryad data repository (doi 10.5061/dryad.pv6df) provided by Szöllősi et al.

Details of the scripts used to simulate alignments and for model fitting are included in Additional data file 2. The simulated alignments and the masked and filtered primate intron alignments are available on request from the authors.

In the context of the simulated dataset used here, we expect that the reconstructed gene trees will become more similar to the species tree than the true trees used to simulate alignments.

Note that like in real studies, these models were far simpler than the models used to simulate the alignments.

The program Seq-Gen [ 64] was used to simulate eight alignments on a tree derived from the HA segment of the Hong Kong data set.

This consists of 600 sets of 32 simulated protein sequences each divided into two categories, asymmetric and symmetric, depending on the original tree topology used to simulate the alignments.

The posterior rates were then estimated using our MCMC approach on both the initial tree (used to simulate the alignment) and the distribution of trees obtained from BEAST.

Specifically, the TFnuGTR model was fitted to the alignment and the resulting parameter MLEs used to simulate 100, 50 kbp long alignments.

(2013b), was constructed using homologous families from the HOGENOM database (Penel et al., 2009) and contains both real and simulated alignments as well as the gene trees used to simulate sequences.

It can be used to simulate anticipatory adaptive behavior.

We then used the 'ppred' function to simulate alignments using the model parameters from the samples in the stationary posterior distribution.