Metadata-Version: 1.0
Name: buddysuite
Version: 1.2b6
Summary: BuddySuite is a collection of command line utilities written in Python for working with biological data.
Home-page: https://github.com/biologyguy/BuddySuite
Author: Stephen Bond
Author-email: steve.bond@gmail.com
License: Public Domain
Description: |Build Status| |Coverage Status| |PyPi version|
        
        |BuddySuite|
        
        --------------
        
        Description
        -----------
        
        The BuddySuite modules are 'one-stop-shop' command line tools for common
        biological data file manipulations. Formats are detected automatically,
        conversions are seamless, and you can pipe into or out of the modules,
        allowing you to spend more time analyzing your sequences, alignments,
        and phylogenetic trees, instead of wrangling them.
        
        For example, the following command reads in three sequence files (all in
        different formats), pulls out records with RefSeq identifiers, calls
        MAFFT to generate an alignment, shifts gaps to force a codon alignment,
        calls RAxML to infer a phylogeny, and then roots the tree at its
        midpoint.
        
        ``$: ﻿seqbuddy seqs1.gb seqs2.embl seqs3.fasta --pull_records "[XN]M" | alignbuddy --generate_alignment mafft | alignbuddy --enforce_triplets | phylobuddy --generate_tree raxmlHPC-SSE3 | phylobuddy --root``
        
        BuddySuite is a Python3 project, developed and extensively tested on
        Linux and Mac OS X. Full release versions are also tested on Windows
        before release, so should work as expected on Vista and above.
        
        Getting started
        ---------------
        
        The simplest way to get up and running is:
        
        .. code:: bash
        
            $: pip install buddysuite
            $: buddysuite -setup
        
        Further instructions are available in the `installation
        guide <https://github.com/biologyguy/BuddySuite/wiki/Installation-Guide>`__.
        
        There is also a short `Beginners'
        Guide <https://github.com/biologyguy/BuddySuite/wiki/Beginners-Guide>`__
        to show you the basics.
        
        Each tool in the BuddySuite has been extensively documented in the
        `wiki <https://github.com/biologyguy/BuddySuite/wiki>`__, complete with
        worked examples and explanations for all arguments/options.
        
        -  `SeqBuddy <https://github.com/biologyguy/BuddySuite/wiki/SeqBuddy>`__
        -  `AlignBuddy <https://github.com/biologyguy/BuddySuite/wiki/AlignBuddy>`__
        -  `PhyloBuddy <https://github.com/biologyguy/BuddySuite/wiki/PhyloBuddy>`__
        -  `DatabaseBuddy <https://github.com/biologyguy/BuddySuite/wiki/DatabaseBuddy>`__
        
        Developers
        ----------
        
        All of the individual Buddy toolkits are located in the 'buddysuite'
        directory and the `'develop'
        branch <https://github.com/biologyguy/BuddySuite/tree/develop>`__ is
        where all new features have been implemented. If you're interested in
        contributing, please refer to the `developer
        page <https://github.com/biologyguy/BuddySuite/wiki/Developers>`__ for
        further information on dependencies and instructions.
        
        Citation
        --------
        
        We are currently working on a `peer reviewed
        manuscript <https://github.com/biologyguy/BuddySuite/tree/develop/manuscript>`__,
        but until then there is a very short application note on bioRxiv that
        can be cited if you use BuddySuite in your work.
        
        `DOI: 10.1101/040675 <http://dx.doi.org/10.1101/040675>`__
        
        Contact
        -------
        
        Any comments you have would be really appreciated. Please feel free to
        add issues in the GitHub issue tracker or contact Steve Bond (lead
        developer) directly at steve.bond@nih.gov.
        
        .. |Build Status| image:: https://travis-ci.org/biologyguy/BuddySuite.svg?branch=master
           :target: https://travis-ci.org/biologyguy/BuddySuite
        .. |Coverage Status| image:: https://coveralls.io/repos/github/biologyguy/BuddySuite/badge.svg?branch=master
           :target: https://coveralls.io/github/biologyguy/BuddySuite?branch=master
        .. |PyPi version| image:: https://img.shields.io/pypi/v/buddysuite.svg
           :target: https://pypi.python.org/pypi/buddysuite
        .. |BuddySuite| image:: https://raw.githubusercontent.com/biologyguy/BuddySuite/master/buddysuite/images/BuddySuite-logo.gif
           :target: https://github.com/biologyguy/BuddySuite/wiki
Keywords: computational biology,computational genetics,genetics,genome,phylogenetics,biology,bioinformatics
Platform: UNKNOWN
