Metadata-Version: 1.0
Name: buddysuite
Version: 1.2b5
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](https://travis-ci.org/biologyguy/BuddySuite.svg?branch=master)](https://travis-ci.org/biologyguy/BuddySuite)
        [![Coverage Status](https://coveralls.io/repos/github/biologyguy/BuddySuite/badge.svg?branch=master)](https://coveralls.io/github/biologyguy/BuddySuite?branch=master)
        <p align="center"><a href="https://github.com/biologyguy/BuddySuite/wiki">
        <img src="https://raw.githubusercontent.com/biologyguy/BuddySuite/master/buddysuite/images/BuddySuite-logo.gif" /></a></p>
        <p align="center">
        <a href="https://github.com/biologyguy/BuddySuite/wiki/SeqBuddy"><img src="https://raw.githubusercontent.com/biologyguy/BuddySuite/master/buddysuite/images/SeqBuddy-logo.gif" width=20%/></a>
        <a href="https://github.com/biologyguy/BuddySuite/wiki/AlignBuddy"><img src="https://raw.githubusercontent.com/biologyguy/BuddySuite/master/buddysuite/images/AlignBuddy-logo.gif" width=25%/></a>
        <a href="https://github.com/biologyguy/BuddySuite/wiki/DatabaseBuddy"><img src="https://raw.githubusercontent.com/biologyguy/BuddySuite/master/buddysuite/images/DBBuddy-logo.gif" width=20%/></a>
        <a href="https://github.com/biologyguy/BuddySuite/wiki/PhyloBuddy"><img src="https://raw.githubusercontent.com/biologyguy/BuddySuite/master/buddysuite/images/PhyloBuddy-logo.gif" width=25%/></a>
        </p>
        <p align="center">Do fun stuff with biological data files. Seriously, biological data is fun stuff :)</p>
        ___
        
        ## 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 tested on Linux and Mac OS X. It should generally work on Windows as well, but
         testing on Windows has been extremely limited.
        
        ## Getting started
        The simplest way to get up and running is:
        
        ```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](mailto:steve.bond@nih.gov).
        
Keywords: computational biology,computational genetics,genetics,genome,phylogenetics,biology,bioinformatics
Platform: UNKNOWN
