{ "info": { "author": "Stephen Bond", "author_email": "steve.bond@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Environment :: Console", "Intended Audience :: Science/Research", "License :: Public Domain", "Natural Language :: English", "Operating System :: MacOS :: MacOS X", "Operating System :: Microsoft :: Windows", "Operating System :: POSIX :: Linux", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3 :: Only", "Topic :: Scientific/Engineering", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Software Development :: Libraries :: Python Modules" ], "description": "|Build_Status| |Coverage_Status| |PyPi_version|\n\n|BuddySuite|\n\n--------------\n\nDescription\n-----------\n\nThe BuddySuite modules are 'one-stop-shop' command-line tools for common\nbiological data file manipulations. Formats are detected automatically,\nconversions are seamless, and you can pipe into or out of the modules to\nbuild custom bioinformatics workflows, allowing you to spend more time analyzing\nyour sequences, alignments, and phylogenetic trees, instead of wrangling them.\n\nFor example, the following command reads in three sequence files (all in\ndifferent formats), pulls out records with RefSeq identifiers, calls\nMAFFT to generate an alignment, shifts gaps to force a codon alignment,\ncalls RAxML to infer a phylogeny, and then roots the tree at its\nmidpoint.\n\n``$: \ufeffseqbuddy seqs1.gb seqs2.embl seqs3.fasta --pull_records \"[XN]M\" | alignbuddy --generate_alignment mafft | alignbuddy --enforce_triplets | phylobuddy --generate_tree raxmlHPC-SSE3 | phylobuddy --root``\n\nBuddySuite is a Python3 project, developed and extensively tested on\nLinux and Mac OS X. Full release versions are also tested on Windows\nbefore release, so should work as expected on Vista and above.\n\nGetting started\n---------------\n\nThe simplest way to get up and running is:\n\n.. code:: bash\n\n $: pip install buddysuite\n $: buddysuite -setup\n\nFurther instructions are available in the `installation\nguide `__.\n\nThere is also a `Beginners'\nGuide `__\nto show you the basics, as well as a more comprehensive\n`Tutorial `__.\n\nEach tool in the BuddySuite has been extensively documented in the\n`wiki `__, complete with\nworked examples and explanations for all arguments/options.\n\n- `SeqBuddy `__\n- `AlignBuddy `__\n- `PhyloBuddy `__\n- `DatabaseBuddy `__\n\nDevelopers\n----------\n\nAll of the individual Buddy toolkits are located in the 'buddysuite'\ndirectory and the `'develop'\nbranch `__ is\nwhere all new features have been implemented. If you're interested in\ncontributing, please refer to the `developer\npage `__ for\nfurther information.\n\nCitation\n--------\n\nIf you use BuddySuite in your work, we would greatly appreciate references to our manuscript:\n\n.. code:: bibtex\n\n @article{doi:10.1093/molbev/msx089,\n author = {Bond, Stephen R. and Keat, Karl E. and Barreira, Sofia N. and Baxevanis, Andreas D.},\n title = {BuddySuite: Command-Line Toolkits for Manipulating Sequences, Alignments, and Phylogenetic Trees},\n journal = {Molecular Biology and Evolution},\n volume = {34},\n number = {6},\n pages = {1543-1546},\n year = {2017},\n doi = {10.1093/molbev/msx089},\n URL = { + http://dx.doi.org/10.1093/molbev/msx089},\n eprint = {/oup/backfile/content_public/journal/mbe/34/6/10.1093_molbev_msx089/1/msx089.pdf}\n}\n\nThrough a series of unfortunate events and a surprisingly unresponsive publishing company, the manuscript is behind a\n paywall... Thank goodness for `pre-prints on bioRxiv