Supplementary data and scripts for the publication "Discovery of numerous novel Helitron-like elements in eukaryote genomes using HELIANO"

##Information of directories. Each directory contains necessary data and scripts to do the corresponding analysis

1. Benchmarking/: benchmarking analysis for heliano. (For Figure 3, Supplementary Table S2)
2. GeneCapture/: analysis for captured genes within HLEs. (For Figure 6, Supplementary Table S11)
3. HLE_model_species/: analysis for heliano results on three model species. (For Table 1, Figure 4, Supplementary Table S5-9, Supplementary Figure 4)
4. HLE_sampled_species/: analysis for heliano results on 404 sampled species. (For Figure 5, Supplementary Table S10, Supplementary Figure 5)
5. hmm_model/: build hmm model for Hel and Rep domains. (For RepHel.hmm that is important to detect and classify HLEs)
6. Phylogenetical_tree/: making phylogenetical trees. (For Figure 1, Supplementary Figure 2-3)
7. Sample_species/: about how to sample species from various genome assemblies. (Supplementary Table S3)
8. HLE_feature/: information about the position of RepHel domain and the length of HLE sequences. (Supplementary Figure 1)