{ "info": { "author": "Eric Talevich", "author_email": "eric.talevich@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Intended Audience :: Science/Research", "License :: OSI Approved :: BSD License", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: Implementation :: PyPy", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "BioCMA\n======\n\nConsensus Multiple Alignment format, using Biopython alignments.\n\nI/O support and relevant functionality for the Consensus Alignment Format (CMA).\nThis format represents protein sequence alignments. It is used by a few tools by\nDr. Andrew F. Neuwald, notably CHAIN_ and MAPGAPS_.\n\n.. _CHAIN: http://chain.igs.umaryland.edu/\n.. _MAPGAPS: http://mapgaps.igs.umaryland.edu/\n\nBiopython objects and conventions are used where possible.\n\n\nInstallation\n------------\n\nThis is an ordinary Python package. You can install it from source with the\nsetup.py script::\n\n python setup.py build\n python setup.py install\n\nStable releases are uploaded to PyPI as well, so you can install BioFrills with\nPython package managers::\n\n pip install biofrills\n\nOr::\n\n easy_install biofrills\n\nSome scripts that I find useful are in the scripts/ directory. By default these\nare not installed, but you can include them by uncommenting the line in setup.py\nthat starts with ``scripts=glob``...\n\nAlternatively, you can just copy those scripts into another directory in your\n``$PATH``.\n\n\nWhat can the CMA format do for me?\n----------------------------------\n\n- Like the A2M and Stockholm formats, alignments are shown with insertions as\n lowercase characters and deletions are dashes\n- Like the A3M format, alignments are pairwise versus a profile (or \"consensus\"\n sequence), which also dictates which sites are indels. By compressing the\n insert columns, a large of alignment of many divergent (but related) sequences\n can be shown without filling it will mostly gap characters, as Stockholm can.\n- Like Stockholm, but unlike A2M and A3M, more than one alignment can be\n contained in a single file.\n- Typically, an ungapped consensus sequence will be included as the first\n sequence.\n- A FASTA-like header contains additional, optional fields for the number of\n leading and trailing sites and NBCI taxonomy codes\n\n\nWho uses CMA?\n-------------\n\nThe CMA format appears to have been invented by Dr. Andrew Neuwald at the\nUniversity of Maryland, and is used in these programs:\n\n- MAPGAPS: http://mapgaps.igs.umaryland.edu/\n- CHAIN: http://chain.igs.umaryland.edu/\n\n\nShould I use CMA in my own work?\n--------------------------------\n\nUnless you're working with MAPGAPS or CHAIN, no.\n\n", "description_content_type": null, "docs_url": null, "download_url": "UNKNOWN", "downloads": { "last_day": -1, 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