.. _`Bio++`: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
.. _`Python`: https://www.python.org
.. _`dms_tools2`: http://jbloomlab.github.io/dms_tools2
.. _`dms_tools2 source code`: https://github.com/jbloomlab/dms_tools2
.. _`preferences file format`: https://jbloomlab.github.io/dms_tools2/dms2_prefs.html#preferences-file
.. _`differential preferences file format`: https://jbloomlab.github.io/dms_tools2/dms2_diffsel.html#site-differential-selection-file
.. _`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
.. _`Jesse Bloom`: https://research.fhcrc.org/bloom/en.html
.. _`Bloom lab`: https://research.fhcrc.org/bloom/en.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
.. _`phydms`: http://jbloomlab.github.io/phydms
.. _`phydms source code`: https://github.com/jbloomlab/phydms
.. _`Yang, Nielsen, Goldman, and Krabbe Pederson, Genetics, 155:431-449`: http://www.genetics.org/content/155/1/431
.. _`Wong et al, Genetics, 168:1041-1051`: http://www.genetics.org/content/168/2/1041
.. _`Bloom, Mol Biol Evol, 31:2753-2769`: http://mbe.oxfordjournals.org/content/31/10/2753
.. _`Bloom, Mol Biol Evol, 31:1956-1978`: http://mbe.oxfordjournals.org/content/31/8/1956
.. _`Bloom, BMC Bioinformatics, 16:168`: http://www.biomedcentral.com/1471-2105/16/168
.. _`Thyagarajan and Bloom, eLife, 3:e03300`: http://elifesciences.org/content/3/e03300
.. _`Doud et al, Mol Biol Evol, 32:2944-2960`: https://dx.doi.org/10.1093/molbev/msv167
.. _`Rodrigue and Lartillot, PNAS, 107:4629-4634`: http://www.pnas.org/content/107/10/4629.full
.. _`Halpern and Bruno, Mol Biol Evol, 15:910-917`: http://www.ncbi.nlm.nih.gov/pubmed/9656490
.. _`McCandlish and Stoltzfus, Quarterly Review of Biology, 89:225-252`: http://www.ncbi.nlm.nih.gov/pubmed/25195318
.. _`HKY85`: https://dx.doi.org/10.1007%2FBF02101694
.. _`Kosakovsky Pond and Frost, Mol Biol Evol, 22:1208-1222`: http://mbe.oxfordjournals.org/content/22/5/1208.full
.. _`AIC`: https://en.wikipedia.org/wiki/Akaike_information_criterion
.. _`reStructuredText`: http://docutils.sourceforge.net/rst.html
.. _`Julien Dutheil`: http://kimura.univ-montp2.fr/jdutheil/CMS/index.php/
.. _`Laurent Gueguen`: https://lbbe.univ-lyon1.fr/-Gueguen-Laurent-.html
.. _`CeCILL`: http://www.cecill.info/licences.en.html
.. _`PyPI`: https://pypi.python.org/pypi
.. _`Gueguen et al, Mol Biol Evol, 30:1745-1750`: http://mbe.oxfordjournals.org/content/30/8/1745
.. _`Crooks et al, Genome Research, 14:1188-1190`: http://genome.cshlp.org/content/14/6/1188
.. _`codonPhyML`: http://sourceforge.net/projects/codonphyml/
.. _`LSD`: http://www.atgc-montpellier.fr/LSD/
.. _`Olivier Gascuel`: http://www.lirmm.fr/~gascuel/
.. _`To et al, Systematic Biology, 65:82-97`: https://dx.doi.org/10.1093/sysbio/syv068
.. _`latex`: https://www.latex-project.org/
.. _`Benjamini-Hochberg`: https://en.wikipedia.org/wiki/False_discovery_rate#Benjamini.E2.80.93Hochberg_procedure
.. _`Goldman and Whelan, Mol Biol Evol, 19:1821-1831`: http://mbe.oxfordjournals.org/content/19/11/1821.long
.. _`Knudsen and Miyamoto, BMC Evol Biol, 5:21`: http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-5-21
.. _`Bloom, Biology Direct, 12:1`: http://biologydirect.biomedcentral.com/articles/10.1186/s13062-016-0172-z
.. _`RAxML`: http://sco.h-its.org/exelixis/web/software/raxml/index.html
.. _`Felsenstein, J Mol Evol, 1981`: http://rd.springer.com/article/10.1007/BF01734359
.. _`Yang, J Mol Evol, 51:423-432`: http://abacus.gene.ucl.ac.uk/ziheng/pdf/2000YangJMEv51p423.pdf
.. _`full list of contributors`: https://github.com/jbloomlab/phydms/contributors
.. _`pyvolve`: http://sjspielman.org/pyvolve/
.. _`Spielman and Wilke, PLoS One, 10:e0139047`: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0139047
.. _`Pond et al, PLoS One, 5:e11230`: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0011230
.. _`Yang, J Mol Evol, 39:306-314`: https://www.ncbi.nlm.nih.gov/pubmed/7932792
.. _`Hilton, Doud, and Bloom, PeerJ, 2017`: https://peerj.com/articles/3657/
