Perl scripts for each transactivation/repression domain model were run against the complete set of protein models from each genome (Supplementary Material online).
This analysis identified matches for more than 14,000 gene models in each genome (BLASTx, bit-score ≥50): 54–67% of gene models in A. digitifera and 48 49% in N. vectensis.
The fits for the models for each genome were compared using Akaike's Information Criterion (AIC) [29].
Predicted, translated gene models for each genome were used and required coverage of 70% of both genes with an e-value of 10-5 an an effective database size of 10.
Each model genome included four diploid chromosomes with 100 loci each.
T-values resulting from the linear model are displayed for each genome feature in the bar plots and indicate significance (shaded grey box equals p > 0.05, Bonferroni-corrected per model) and direction of the correlation.
In the case of human mitochondria, the model of replication where each genome acts as an individual unit and replicates independently, even while being part of a focus appears as the one most satisfying the observed kinetics.
Maximum likelihood phylogenetic trees were obtained with PHYML 2.4.4 [94] using the previously determined models of nucleotide substitution for each genome region and sample, and support for the nodes were evaluated by bootstrapping with 1000 pseudorreplicates.
(8) Projecting the 3D genome model to generate 60 projection images for each genome image according to the 60 equivalent icosahedral orientations of the capsid.
Thus, chloroplast genomes provide an ideal example for modeling genome rearrangements over a broad evolutionary time scale.
