Scripts and pipelines associated with the submitted publication: Osmanski et al. 2021. Insights into mammalian TE diversity via the curation of 200+ mammalian genome assemblies. Science: submitted.
Pipeline used to run RepeatMasker on all zoonomia assemblies
Pipleline used to convert repeatmasker output to .bed format. This pipeline merges overlapping hits based using 'lower_divergence' criterion.
Workflow used to create the Figure S1 in Christmas et al. 2021. Evolutionary constraint and innovation across hundreds of placental mammals. Science.
Workflow used to create figure 2. A phylogeny with stacked bar charts as tree tips depicting the proportions of various TE types found within the respective assembly.
Creates ultrametric phylogeny used for subsequent hierarchical Bayesian analyses.
Workflow used to create Figure 4. A phylogeny with stacked bar chart tree tips depicting the TE content of Chiropterans.
Runs the hierarchical Bayesian analyses behind figure 5.
Workflow used to plot figure 5. The recent mamammlian TE diversity using both Shannon's H & Pielou's J
Runs the hierarchical Bayesian analyses behind figure 6.
Workflow used to plot figure 6. Plot depicting recent DNA transposon accumulation among three dietary phenotypes: carnivore, herbivore, & omnivore.