This repository harbors data and documented scripts corresponding to the analyses conducted in the following manuscript:
Scott William Roy, Landen Gozashti, Bradley A. Bowser and Brooke N. Weinstein, Graham E. Larue (2020). Massive intron gain in the most intron-rich eukaryotes is driven by introner transposable elements of unprecedented diversity and flexibility. BioRxiv https://doi.org/10.1101/2020.10.14.339549
The folder, intron_models, contains the alignment files and phylogenetic tree file to reproduce the ancestral intron reconstruction in the paper using the graphical user interface in Malin along with results from the analyses.
The folder, ILEs, contains fasta files of sequences for each ILE family initially identified in each considered species, along with consensus sequences for each ILE family and candidate ILE sequences found in intergenic regions. The folder also contains the custom perl scripts used to initially identify ILEs from annotated genomes and identify phase bias with regard to new insertions. Furthermore, we provide a series of python scripts used to construct consensus sequences for ILE families and retrieve candidate insertions in intergenic regions.