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

Project description

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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 to
build custom bioinformatics workflows, 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

``$: seqbuddy 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 <>`__.

There is also a `Beginners'
Guide <>`__
to show you the basics, as well as a more comprehensive
`Tutorial <>`__.

Each tool in the BuddySuite has been extensively documented in the
`wiki <>`__, complete with
worked examples and explanations for all arguments/options.

- `SeqBuddy <>`__
- `AlignBuddy <>`__
- `PhyloBuddy <>`__
- `DatabaseBuddy <>`__


All of the individual Buddy toolkits are located in the 'buddysuite'
directory and the `'develop'
branch <>`__ is
where all new features have been implemented. If you're interested in
contributing, please refer to the `developer
page <>`__ for
further information.


If you use BuddySuite in your work, we would greatly appreciate references to our manuscript:

.. code:: bibtex

author = {Bond, Stephen R. and Keat, Karl E. and Barreira, Sofia N. and Baxevanis, Andreas D.},
title = {BuddySuite: Command-Line Toolkits for Manipulating Sequences, Alignments, and Phylogenetic Trees},
journal = {Molecular Biology and Evolution},
volume = {34},
number = {6},
pages = {1543-1546},
year = {2017},
doi = {10.1093/molbev/msx089},
URL = { +},
eprint = {/oup/backfile/content_public/journal/mbe/34/6/10.1093_molbev_msx089/1/msx089.pdf}

Through a series of unfortunate events and a surprisingly unresponsive publishing company, the manuscript is behind a
paywall... Thank goodness for `pre-prints on bioRxiv <`__ !



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

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