.. _`Python`: https://www.python.org
.. _`dms_tools2`: http://jbloomlab.github.io/dms_tools2
.. _`dms_tools2 source code`: https://github.com/jbloomlab/dms_tools2
.. _`PyStan`: http://pystan.readthedocs.org/en/latest/
.. _`GelmanRubin1992`: http://www.jstor.org/stable/2246093
.. _`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
.. _`Bloom lab`: https://research.fhcrc.org/bloom/en.html
.. _`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
.. _`phydms`: http://jbloomlab.github.io/phydms
.. _`phydms source code`: https://github.com/jbloomlab/phydms
.. _`reStructuredText`: http://docutils.sourceforge.net/rst.html
.. _`PyPI`: https://pypi.python.org/pypi
.. _`Crooks et al, Genome Research, 14:1188-1190`: http://genome.cshlp.org/content/14/6/1188
.. _`full list of contributors`: https://github.com/jbloomlab/dms_tools2/contributors
.. _`Doud and Bloom (2016)`: http://www.mdpi.com/1999-4915/8/6/155
.. _`Doud et al (2018)`: https://www.nature.com/articles/s41467-018-03665-3
.. _`Haddox et al (2018)`: https://elifesciences.org/articles/34420
.. _`Doud2016 example`: https://github.com/jbloomlab/dms_tools2/blob/master/examples/Doud2016/analysis_notebook.ipynb
.. _`Doud2017 example`: https://github.com/jbloomlab/dms_tools2/blob/master/examples/Doud2017/analysis_notebook.ipynb
.. _`Dingens2017 example`: https://github.com/jbloomlab/dms_tools2/blob/master/examples/Dingens2017/analysis_notebook.ipynb
.. _`Dingens2018 example`: https://github.com/jbloomlab/dms_tools2/blob/master/examples/Dingens2018/analysis_notebook.ipynb
.. _`Doud2018 example`: https://github.com/jbloomlab/dms_tools2/blob/master/examples/Doud2018/analysis_notebook.ipynb
.. _`Haddox2018 example`: https://github.com/jbloomlab/dms_tools2/tree/master/examples/Haddox2018
.. _`Lee2018 example`: https://github.com/jbloomlab/dms_tools2/tree/master/examples/Lee2018
.. _`Jupyter notebook`: https://ipython.org/notebook.html
.. _`fastq-dump`: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=fastq-dump
.. _`Sequence Read Archive`: https://www.ncbi.nlm.nih.gov/sra
.. _`slurm`: https://slurm.schedmd.com/
.. _`comprehensive codon mutagenesis`: https://github.com/jbloomlab/CodonTilingPrimers
.. _`Hiatt et al (2010)`: https://www.nature.com/nmeth/journal/v7/n2/full/nmeth.1416.html
.. _`Kinde et al (2011)`: http://www.pnas.org/content/108/23/9530.short
.. _`Jabara et al (2011)`: http://www.pnas.org/content/108/50/20166.short
.. _`Wu et al (2014)`: https://www.ncbi.nlm.nih.gov/pubmed/24820965
.. _`Zhang et al (2016)`: https://www.ncbi.nlm.nih.gov/pubmed/26868371
.. _`Dingens et al (2018)`: https://doi.org/10.1371/journal.ppat.1007159
.. _`Lee et al (2018)`: http://dx.doi.org/10.1101/298364
.. _`Dingens et al (2017)`: http://dx.doi.org/10.1016/j.chom.2017.05.003
.. _`Haddox et al (2016)`: http://dx.doi.org/10.1371/journal.ppat.1006114
.. _`Doud et al (2017)`: http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1006271
.. _`Bloom (2015)`: http://www.biomedcentral.com/content/pdf/s12859-015-0590-4.pdf
.. _`Bloom (2014)`: http://mbe.oxfordjournals.org/content/31/8/1956
.. _`Bloom (2017)`: https://biologydirect.biomedcentral.com/track/pdf/10.1186/s13062-016-0172-z?site=biologydirect.biomedcentral.com
.. _`Hilton et al (2017)`: https://peerj.com/articles/3657.pdf
.. _`ggseqlogo`: https://omarwagih.github.io/ggseqlogo/
.. _`reference for ggseqlogo`: https://doi.org/10.1093/bioinformatics/btx469
.. _`rplot module`: https://jbloomlab.github.io/dms_tools2/dms_tools2.rplot.html
.. _`minimap2 module`: https://jbloomlab.github.io/dms_tools2/dms_tools2.minimap2.html
.. _`minimap2`: https://github.com/lh3/minimap2
.. _`reference for minimap2`: https://doi.org/10.1093/bioinformatics/bty191
.. _`dmslogo`: https://jbloomlab.github.io/dmslogo/
