Metadata-Version: 1.1
Name: PyPhyloGenomics
Version: 0.3.6
Summary: Tools to work in phylogenomics, from NSG group http://nymphalidae.utu.fi
Home-page: http://carlosp420.github.com/PyPhyloGenomics/
Author: Carlos Pena, Victor Solis, Pavel Matos, Chris Wheat
Author-email: mycalesis@gmail.com
License: GPL v3
Download-URL: http://carlosp420.github.com/PyPhyloGenomics/
Description: PyPhyloGenomics
        ===============
        
        A package to work on Phylogenomics.
        
        [[In development.]]
        
        Developers
        ----------
        
        -   Carlos Peña (email: carlos.pena@utu.fi)
        -   Victor Solis
        -   Pavel Matos
        -   Chris Wheat
        
        Installing PyPhyloGenomics
        --------------------------
        
        PyPhyloGenomics has been developed in Python v2.7. The installer of
        PyPhyloGenomics will try to download and install all its dependencies as
        well. To install PyPhyloGenomics use setup.py:
        
            python setup.py build  
            python setup.py install
        
        If it fails you can install the dependencies manually:
        
        Install dependencies:
        ---------------------
        
        requests:
        
        The package requests from here. Or try:
        
            sudo apt-get install python-requests
        
        Parallel Python (pp):
        
        If you are using Ubuntu Linux or related:
        
            sudo apt-get install python-pp
        
        Otherwise, download the source code and install pp:
        
            unzip pp-1.6.4.zip
            cd pp-1.6.4
            python setup.py install
        
        BioPython:
        
        Download and install from here. Or:
        
            sudo apt-get install python-biopython
        
        BeatutifulSoup
        
        Download and install from here. Or:
        
            sudo apt-get install python-bs4
        
        MUSCLE
        
        It is necessary that you install MUSCLE so that PyPhyloGenomics can use
        it to align sequences. Download and install from here.
        
        If you are using Windows you can download the executable file
        muscle3.8.31_i86win32.exe and save it in your Python folder (C:27) as
        muscle.exe.
        
        BLAST
        
        Download and install the BLAST+ executables from the NCBI website. Or
        try:
        
            sudo apt-get install ncbi-blast+
        
        fastx-toolkit
        
        Download and install from here. Or:
        
            sudo apt-get install fastx-toolkit
        
        Reading PyPhyloGenomics' documentation:
        ---------------------------------------
        
        Read the online documentation here:
        http://carlosp420.github.io/PyPhyloGenomics/
        
        Or, after installling do the following:
        
            cd doc  
            make html
        
        Then open the file _build/html/index.html in your web-browser.
        
        Reproduce our analysis:
        -----------------------
        
        You can reproduce all the steps detailed in our [Getting started with
        PyPhylogenomics] guide. Just use the command line in the same folder as
        the Makefile and type make ???
        
Keywords: DNA,genomics,genomes,phylogenetics,genes
Platform: UNKNOWN
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2)
Classifier: Operating System :: OS Independent
Classifier: Environment :: Console
