Metadata-Version: 1.1
Name: phydms
Version: 1.2.5
Summary: Phylogenetic analyses informed by deep mutational scanning data.
Home-page: http://jbloomlab.github.io/phydms
Author: the Bloom lab (see https://github.com/jbloomlab/phydms/contributors for all contributors)
Author-email: jbloom@fredhutch.org
License: GPLv3
Download-URL: https://github.com/jbloom/phydms/tarball/1.2.5
Description: ========================
        ``phydms``
        ========================
        ``phydms`` enables **phy**\logenetic analyses using **d**\eep **m**\utational **s**\canning data to inform the substitution models. It implements **Exp**\erimentally informed **c**\odon **m**\odels (*ExpCM*) for phylogenetic inference and the detection of biologically interesting selection.
        
        ``phydms`` is written by `Jesse Bloom`_, and uses the `Bio++`_ libraries for likelihood calculations (thanks to `Julien Dutheil`_ and `Laurent Gueguen`_ for making these wonderful libraries available).
        
        See the `phydms documentation`_ for information about using ``phydms`` and details about the recommended installation process.
        
        The `phydms source code`_ is freely available under a `GPLv3`_ license (the `Bio++`_ and `LSD`_ source code is packaged into the `phydms source code`_; these code bases are themselves under a `GPL-compatible`_ `CeCILL`_ license and a `GPLv3`_ license, respectively). 
        
        
        .. _`Jesse Bloom`: http://research.fhcrc.org/bloom/en.html
        .. _`Bio++`: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
        .. _`phydms documentation`: http://jbloomlab.github.io/phydms/
        .. _`phydms source code`: https://github.com/jbloomlab/phydms
        .. _`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
        .. _`GPL-compatible`: https://www.gnu.org/licenses/license-list.html#GPLCompatibleLicenses
        .. _`GPLv3`: http://www.gnu.org/copyleft/gpl.html
        .. _`LSD`: http://www.atgc-montpellier.fr/LSD/
        
Platform: Linux
