Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files
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buddysuite
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README.md

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Do fun stuff with biological data files. Seriously, biological data is fun stuff :)


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 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 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:

$: 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.

Developers

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.

Citation

doi

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

@article{doi:10.1093/molbev/msx089,
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 = { + http://dx.doi.org/10.1093/molbev/msx089},
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!

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.