jphmm_tools provides methods for extracting information from jpHMM [Schulz et al. NAR 2012] output.
It implements tool for
- converting Los Alamos alignment file into a reference file suitable for jpHMM:
jphmm_ref -h- aligning sequences based on the jpHMM output:
jphmm_align -h- extracting sequence subtype information from the jpHMM output:
jphmm_subtype -h