Metadata-Version: 1.1
Name: trifusion
Version: 0.5.0.post5
Summary: Streamlining phylogenomic data gathering, processing and visualization
Home-page: https://github.com/ODiogoSilva/TriFusion
Author: Diogo N Silva
Author-email: odiogosilva@gmail.com
License: GPL3
Description: Warning
        -------
        
        | TriFusion is still in active development, so the releases are quite a
          bit out of date
        | and the install scripts and steps may not be properly working. If you
          have any issues,
        | please contact me directly.
        
        TriFusion
        ---------
        
        Website: http://odiogosilva.github.io/TriFusion/
        
        | |Build Status|
        | |Code Health|
        | |codecov|
        
        Streamlining phylogenomic data gathering, processing and visualization
                                                                              
        
        TriFusion is a GUI and command line application designed to streamline
        the workflow of phylogenomic projects. With the dramatic increase in
        size of data sets for phylogenetics and population genetics, programming
        has become a crucial tool to gather, process and analyze the data.
        However, this may still represent a hurdle that precludes the execution
        of such projects by a broader range of researchers. TriFusion aims to
        mitigate this issue by providing a user-friendly visual interface that
        empowers users without any programming knowledge with a set of tools and
        operations that can handle large sets of data.
        
        TriFusion is an open source, cross-platform application written in
        `Python 2.7 <https://www.python.org/>`__ and using the
        `Kivy <https://github.com/kivy/kivy>`__ framework to construct graphical
        interface.
        
        Installation
        ~~~~~~~~~~~~
        
        Executables binaries
        ^^^^^^^^^^^^^^^^^^^^
        
        The latest stable release of TriFusion can be installed as a standalone
        application using one of the following installers.
        
        Linux
        '''''
        
        -  Debian package based (`See
           list <https://en.wikipedia.org/wiki/Category:Debian-based_distributions>`__):
           `trifusion-bin-0.4.11-linux.deb <https://github.com/ODiogoSilva/TriFusion/releases/download/0.4.11/trifusion-bin-0.4.11-linux.deb>`__
        
        -  RPM package based (`See
           list <https://en.wikipedia.org/wiki/Category:RPM-based_Linux_distributions>`__):
           `trifusion-bin-0.4.11-linux.rpm <https://github.com/ODiogoSilva/TriFusion/releases/download/0.4.11/trifusion-bin-0.4.11-linux.rpm>`__
        
        -  ArchLinux/Manjaro (`See
           list <https://wiki.archlinux.org/index.php/Arch_based_distributions>`__):
           `trifusion-bin-0.4.11 <https://aur.archlinux.org/packages/trifusion-bin/>`__
           is available on AUR.
        
        Windows
        '''''''
        
        -  `TriFusion-0.4.12 64bit
           installer <https://github.com/ODiogoSilva/TriFusion/releases/download/0.4.11/TriFusion-v0.4.12-windows64.msi>`__
        -  `TriFusion-0.4.12 32bit
           installer <https://github.com/ODiogoSilva/TriFusion/releases/download/0.4.11/TriFusion-v0.4.12-windows32.msi>`__
        
        Note for Windows 8.x and 10 users:
                                          
        
        Executing the TriFusion installer may generate a warning from
        SmartScreen. To continue with the installation, click the "More info"
        label and then "Run anyway".
        
        Installation from source
        ^^^^^^^^^^^^^^^^^^^^^^^^
        
        TriFusion can be installed directly from source (whether from the latest
        stable release or from the git version), which has its advantages:
        
        -  Stay on the bleeding edge of the application's development (Git
           version)
        
        -  Minimize the application size install
        
        -  Modify the code any way you want. Contributions are welcome.
        
        `Here are instructions on how to install TriFusion from
        source <https://github.com/ODiogoSilva/TriFusion/wiki/Install-from-source>`__.
        (Go ahead, it won't bite.)
        
        How to use
        ~~~~~~~~~~
        
        GUI version
        ^^^^^^^^^^^
        
        Windows
        '''''''
        
        TriFusion should be available in the Start Menu, ready to launch.
        
        Linux
        '''''
        
        If TriFusion was installed using package managers, a TriFusion shortcut
        should have been created and available using your distribution's
        application launcher (Under the Science category). Alternatively,
        TriFusion can be executed from the terminal with the command
        ``TriFusion``.
        
        Command line versions
        ^^^^^^^^^^^^^^^^^^^^^
        
        Command line versions for each of the three modules in TriFusion are
        only available when installing the program from source. Once installed,
        each module can be executed in the terminal using the following
        commands:
        
        -  Orthology search module:
        
           ``orthomcl_pipeline``
        
        -  Process module:
        
           ``TriSeq``
        
        -  Statistics module:
        
           ``TriStats``
        
        For more information on the command line versions, see the manual.
        
        Documentation
        ~~~~~~~~~~~~~
        
        You can download TriFusion User Guide
        `here <https://github.com/ODiogoSilva/TriFusion/raw/master/docs/manual.pdf>`__.
        
        Citation
        ~~~~~~~~
        
        When using OrthoMCL to find ortholog clusters, please cite the original
        software:
        
        Fischer, S., Brunk, B. P., Chen, F., Gao, X., Harb, O. S., Iodice, J.
        B., Shanmugam, D., Roos, D. S. and Stoeckert, C. J. Using OrthoMCL to
        Assign Proteins to OrthoMCL-DB Groups or to Cluster Proteomes Into New
        Ortholog Groups Current Protocols in Bioinformatics. 2011
        35:6.12.1–6.12.19.
        
        Coming soon!
        
        .. |Build Status| image:: https://travis-ci.org/ODiogoSilva/TriFusion.svg?branch=master
           :target: https://travis-ci.org/ODiogoSilva/TriFusion
        .. |Code Health| image:: https://landscape.io/github/ODiogoSilva/TriFusion/master/landscape.svg?style=flat
           :target: https://landscape.io/github/ODiogoSilva/TriFusion/master
        .. |codecov| image:: https://codecov.io/gh/ODiogoSilva/TriFusion/branch/master/graph/badge.svg
           :target: https://codecov.io/gh/ODiogoSilva/TriFusion
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Natural Language :: English
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
