Chun Shen Lim, Brooke N. Weinstein, Scott W. Roy, Chris M. Brown. (2021). Analysis of fungal genomes reveals commonalities of intron loss or gain and functions in intron-poor species. Mol Biol Evol. DOI: https://doi.org/10.1093/molbev/msab094.

This repository contains the Jupyter notebooks and data for our analyses.

• Jupyter notebooks and timetrees for phylogenetic independent contrasts analysis.
• Jupyter notebooks and annotation files for intron site histories analysis.
• A Jupyter notebook and datasets for enrichment analysis of repeat elements.
• Input files for Malin: sequence alignment files for 1,444 sets of orthologs, and a taxa tree.
• Intermediate files generated using Malin: intron table and rate files.
• Output files and results for the inference of ancestral introns.
• A custom GTF file of UTR annotation for Saccharomyces cerevisiae.