Metadata-Version: 1.1
Name: PyPhyloGenomics
Version: 0.3.0
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](http://docs.python-requests.org/en/latest/user/install/). 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](http://www.parallelpython.com/content/view/15/30/) 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](http://biopython.org/wiki/Download). Or:
        
            sudo apt-get install python-biopython
        
        ### BeatutifulSoup
        Download and install from [here](http://www.crummy.com/software/BeautifulSoup/). 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](http://www.drive5.com/muscle/downloads.htm).
        
        If you are using Windows you can download the executable file **muscle3.8.31_i86win32.exe** 
        and save it in your Python folder (C:\Python27\) as **muscle.exe**.
        
        ### BLAST
        Download and install the BLAST+ executables from the
        [NCBI website](http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download). Or try:
        
            sudo apt-get install ncbi-blast+
        
        ### fastx-toolkit
        Download and install from [here](http://hannonlab.cshl.edu/fastx_toolkit/). Or:
        
            sudo apt-get install fastx-toolkit
        
        ## Reading PyPhyloGenomics' documentation:
        Read the online documentation here: [http://carlosp420.github.io/PyPhyloGenomics/](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
