jphmm-tools

Tools for extracting information from jpHMM (http://jphmm.gobics.de) output.


Keywords
jpHMM, HIV, subtyping, recombinants, recombination
License
GPL-3.0
Install
pip install jphmm-tools==0.1.2

Documentation

jpHMM tools

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