buddysuite 1.2b5

BuddySuite is a collection of command line utilities written in Python for working with biological data.

[](https://travis-ci.org/biologyguy/BuddySuite)
[](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 [[e-mail]](mailto:[e-mail]).