.. _anaconda: http://docs.continuum.io/anaconda/install.html
.. _bedtools: http://bedtools.readthedocs.org/en/latest/
.. _bwa: http://bio-bwa.sourceforge.net/
.. _conda: http://docs.continuum.io/conda/
.. _Cython: http://www.cython.org
.. _eatonAndRee: http://sysbio.oxfordjournals.org/content/62/5/689.full
.. _gitter: https://gitter.im/dereneaton/ipyrad
.. _hdf5: https://www.hdfgroup.org/HDF5
.. _H5py: http://www.h5py.org
.. _instructions_here: http://conda.pydata.org/docs/installation.html
.. _ipyparallel: https://github.com/ipython/ipyparallel
.. _ipyrad: https://ipyrad.readthedocs.org/
.. _jupyter: http://jupyter.org/
.. _miniconda: http://repo.continuum.io/miniconda/
.. _mpich: http://www.mpich.org/
.. _muscle: http://www.drive5.com/muscle/
.. _Numpy: http://www.numpy.org/
.. _oaks: https://github.com/dereneaton/virentes  
.. _Pandas: http://pandas.pydata.org/
.. _pyrad: https://github.com/dereneaton/pyrad  
.. _samtools: http://www.htslib.org/
.. _Scipy: https://www.scipy.org/
.. _Sphinx: http://sphinx-doc.org/
.. _Toyplot: https://github.com/sandialabs/toyplot
.. _vsearch: https://github.com/torognes/vsearch
.. _weighted_quartets: https://sysbio.oxfordjournals.org/content/64/2/233.abstract