FlaHMM

FlaHMM is a standalone tool which identifies candidate unistrand flamenco-like piRNA clusters from transposon annotations.

GitHub: https://github.com/Hannon-lab/FlaHMM
Reference: Trapotsi M-A, van Lopik J, Hannon G J, Czech Nicholson B, Bornelöv S (2024) FlaHMM: unistrand flamenco-like piRNA cluster prediction in Drosophila species using hidden Markov models. NAR Genomics and Bioinformatics 6:3:lqae119.
Paper link: https://doi.org/10.1093/nargab/lqae119

We have also prepared a separate GitHub page with detailed instructions on how to re-train FlaHMM from scratch:
https://github.com/Hannon-lab/FlaHMM-supplement