HlaTools is a python package of tools for analyzing and phasing large amplicons of genomic sequence. Primarily this has been developed and tested on the HLA genes from the human MHC region, but the same approach should work for most complex regions of the human genome where phasing is important.

For the primary tools provided by the HlaTools package, we require 5 other python packages as dependencies:
Numpy: http://www.numpy.org/
PBcore: http://github/PacificBiosciences/pbcore.git
PypeFlow: http://github/cschin/pypeFLOW.git
PBdagcon: http://github/PacificBiosciences/pbdagcon.git
PhasingTools: http://github/bnbowman/PhasingTools.git

All 5 packages can be quickly and easily installed with pip:
$ pip install numpy # For NumPy, which is in PyPi
$ pip install git+<GitHub URL> # For all other packages

The other major script included in HlaTools is a pipeline for de-convoluting complex HLA amplicon samples with a mixture of Class I and Class II genes or amplicons with large discrepancies in length. This pipeline is built upon HBAR, formerly known as HGAP, and therefore also requires the HBAR development package in order to use. The HBAR-DTK itself has a fairly intensive installation procedure, detailed in the README distributed with the tool from the HBAR-DTK github page:
http://github.com/PacificBiosciences/HBAR-DTK.git

In addition, this pipeline also wraps two simpler commandline utilites: Blasr for the alignment of reads and Cd-Hit-Est for the reduction of redundancy:
https://github.com/PacificBiosciences/blasr.git
http://weizhong-lab.ucsd.edu/cd-hit/