PROmiRNA - a program for miRNA promoter prediction based on NGS data and semi-supervised learning.
Developed by Annalisa Marsico link to downloadable version
ssHMM - a program for finding sequence-structure motifs from a set of RNA sequences using HMMs and Gibbs sampling. Optimized to work with CLIP-seq data
Developed by Davide Heller Github link to downloadable version
PureCLIP - a statistical model for calling RBP-RNA binding sites from single nucleotide resolution CLIP-seq data based on HMMs and generalized linear models
Developed by Sabrina Krakau Github link to downloadable version