Metadata-Version: 2.1
Name: jphmm-tools
Version: 0.1
Summary: Tools for extracting information from jpHMM (http://jphmm.gobics.de) output.
Home-page: https://github.com/evolbioinfo/jphmm_tools
Author: Anna Zhukova
Author-email: anna.zhukova@pasteur.fr
License: UNKNOWN
Keywords: jpHMM,HIV,subtyping,recombinants
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Description-Content-Type: text/markdown
Requires-Dist: pandas
Requires-Dist: numpy
Requires-Dist: biopython

# jpHMM tools

__jphmm_tools__ provides methods for extracting information 
from [jpHMM](http://jphmm.gobics.de) [[Schulz *et al.* NAR 2012]](https://academic.oup.com/nar/article/40/W1/W193/1073895) output.

It implements tool for
* converting [Los Alamos](https://www.hiv.lanl.gov/content/sequence/HIV/mainpage.html) alignment file
into a reference file suitable for jpHMM:
```bash
jphmm_ref -h
```
* aligning sequences based on the jpHMM output:
```bash
jphmm_align -h
```
* extracting sequence subtype information from the jpHMM output:
```bash
jphmm_subtype -h
```


