Sequence sets, alignments and raw tree files for the structure-guided evolutionary analysis of group I introns

Datasets, alignments and tree files used to create figure 3 and supplementary figure S1 of the paper:
1. Entire set of analyzed introns (GIISSD database + introns identified in Bastillevirinae).
2. Non-redundant introns (cd-hit -i GIISSD_and_Bastille.fasta -o GIISSD_and_Bastille.unique_099.fasta -c 0.99 -s 0.99 -M 1000).
3. Original structure-guided alignment of the non-redundant intron set and RFAM group I model (cmalign -o Unique_vs_RF00028.sto --dnaout --mxsize 5140 --cpu 30 --matchonly --outformat Stockholm RF00028.cm GIISSD_and_Bastille.unique_099.fasta) and a version converted to fasta (./sto2fasta.py -s Unique_vs_RF00028.sto).
4. Pruned alignment (sites with more than 50% gaps removed using Geneious "mask alignment" tool, poorly aligned introns filtered out by: ./prune_alignment.py -f Unique_vs_RF00028.fasta -l 50).
5. Maximum likelihood and consensus trees of conserved intron elements (iqtree -nt AUTO -s Unique_vs_RF00028.pruned.fasta -alrt 1000 -bb 1000).
(Scripts used in the study are available from https://github.com/zwmuam/Bastilevirinae_introns)