These R scripts have been published in Hua et al., Plant J (2018) 95, 296–311 to study the duplication mechanism of the ubiquitin and ubiquitin-like protein families. Superfamily annotation was performed using ctt package available in a seperate repository.
Reference
Hua Z, Doroodian P, Vu W. Contrasting duplication patterns reflect functional diversities of ubiquitin and ubiquitin-like protein modifiers in plants. Plant J. 2018;95(2):296-311. Epub 2018/05/09. doi: 10.1111/tpj.13951. PubMed PMID: 29738099.