Tree-HMM is an extension of the popular ChromHMM for doing clustering of epigenetic markers. Given a complete set of epigenetic markers for several cell types, and the phylogeny describing their relationship, Tree-HMM will perform approximate inference on the graphical model induced by connecting genomic positions of a certain cell type in a chain while also connecting different species according to the tree.
CBCL Lab (Computational Biology and Computational Learning) @ UCI
- Linux/ Windows/MacOsX
:: MORE INFORMATION
BMC Bioinformatics. 2013;14 Suppl 5:S4. doi: 10.1186/1471-2105-14-S5-S4. Epub 2013 Apr 10.
Discovering and mapping chromatin states using a tree hidden Markov model.
Biesinger J1, Wang Y, Xie X.