.. _`Python`: https://www.python.org
.. _`dms_tools`: http://jbloom.github.io/dms_tools
.. _`dms_tools source code`: https://github.com/jbloom/dms_tools
.. _`mapmuts`: http://jbloom.github.io/mapmuts
.. _`PyStan`: http://pystan.readthedocs.org/en/latest/
.. _`GelmanRubin1992`: http://www.jstor.org/stable/2246093
.. _`Firnberg2012`: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0052031
.. _`Kronecker delta`: http://en.wikipedia.org/wiki/Kronecker_delta
.. _`Hadamard product`: http://en.wikipedia.org/wiki/Hadamard_product_(matrices)
.. _`Multinomial`: http://en.wikipedia.org/wiki/Multinomial_distribution
.. _`Dirichlet`: http://en.wikipedia.org/wiki/Dirichlet_distribution
.. _`MCMC`: http://en.wikipedia.org/wiki/Markov_chain_Monte_Carlo
.. _`weblogo`: https://code.google.com/p/weblogo/
.. _`reference for weblogo`: http://genome.cshlp.org/content/14/6/1188
.. _`Jesse Bloom`: labs.fhcrc.org/bloom
.. _`Wu et al (2014)`: http://jvi.asm.org/content/88/17/10157
.. _`Thyagarajan and Bloom (2014)`: http://elifesciences.org/content/3/e03300
.. _`Melnikov et al (2014)`: http://nar.oxfordjournals.org/content/42/14/e112
.. _`Fowler and Fields (2014)`: http://www.nature.com/nmeth/journal/v11/n8/full/nmeth.3027.html
.. _`statistical bias inherent in ratio estimation`: http://en.wikipedia.org/wiki/Ratio_estimator
.. _`biological replicates`: http://www.nature.com/nmeth/journal/v11/n9/full/nmeth.3091.html
.. _`GPL-compatible`: https://www.gnu.org/licenses/license-list.html#GPLCompatibleLicenses
.. _`pip`: https://pypi.python.org/pypi/pip
.. _`Python convention for local installation`: https://www.python.org/dev/peps/pep-0370/
.. _`bash shell`: http://www.gnu.org/software/bash/
.. _`GPLv3`: http://www.gnu.org/copyleft/gpl.html
.. _`scipy`: http://www.scipy.org/
.. _`numpy`: http://www.numpy.org/
.. _`matplotlib`: http://matplotlib.org/
.. _`Biopython`: http://biopython.org/wiki/Main_Page
.. _`cython`: http://cython.org/
.. _`weblogolib`: https://code.google.com/p/weblogo/
.. _`PyPDF2`: https://pypi.python.org/pypi/PyPDF2
