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Overview

The tutorials below demonstrate the main ConsHMM functionalities.

Since ConsHMM was built on top of ChromHMM, we recommend referencing the ChromHMM User Manual for additional details regarding the underlying ChromHMM functions.

Tutorials

• ConsHMM Segmentation Tutorials:

  • Reference-based ConsHMM Segmentation Tutorial: how to learn a ConsHMM model and produce a segmentation of the reference genome from a multiple sequence alignment, demonstrated using the hg19 Multiz 100-way alignment from the original ConsHMM paper (Arneson and Ernst, Communications Biology, 2019).
  • Allele-specific ConsHMM Segmentation Tutorial: how to create an allele-specific ConsHMM segmentation, using a learned model, demonstrated using the hg38 Multiz 100-way alignment

• External Enrichments Tutorial: how to compute the enrichment of the the states in a genome segmentation for other external annotations.