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– Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.\n    :target: https://www.repostatus.org/#wip\n\n.. image:: https://travis-ci.com/robertopreste/allfreqs.svg?branch=master\n        :target: https://travis-ci.com/robertopreste/allfreqs\n\n.. image:: https://readthedocs.org/projects/allfreqs/badge/?version=latest\n        :target: https://allfreqs.readthedocs.io/en/latest/?badge=latest\n        :alt: Documentation Status\n\n\nCalculate allele frequencies from a sequence multialignment.\n\n\n* Free software: MIT license\n* Documentation: https://allfreqs.readthedocs.io\n* GitHub repo: https://github.com/robertopreste/allfreqs\n\n\nFeatures\n========\n\nCalculate allele frequencies from a nucleotide multialignment in fasta or csv format.\n\nAllele frequencies will be returned as a table in which each row is a nucleotide position (based on\nthe provided reference sequence) and columns are A, C, G, T frequencies as well as gaps and other\nnon-canonical nucleotides.\n\nFor example, given the following multialignment:\n\n+------+----------+\n| ID   | Sequence |\n+======+==========+\n| ref  | ACGTACGT |\n+------+----------+\n| seq1 | A-GTAGGN |\n+------+----------+\n| seq2 | ACCAGCGT |\n+------+----------+\n\nthe resulting allele frequencies will be:\n\n+----------+-----+-----+-----+-----+-----+-----+\n| position | A   | C   | G   | T   | gap | oth |\n+==========+=====+=====+=====+=====+=====+=====+\n| 1.0_A    | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |\n+----------+-----+-----+-----+-----+-----+-----+\n| 2.0_C    | 0.0 | 0.5 | 0.0 | 0.0 | 0.5 | 0.0 |\n+----------+-----+-----+-----+-----+-----+-----+\n| 3.0_G    | 0.0 | 0.5 | 0.5 | 0.0 | 0.0 | 0.0 |\n+----------+-----+-----+-----+-----+-----+-----+\n| 4.0_T    | 0.5 | 0.0 | 0.0 | 0.5 | 0.0 | 0.0 |\n+----------+-----+-----+-----+-----+-----+-----+\n| 5.0_A    | 0.5 | 0.0 | 0.5 | 0.0 | 0.0 | 0.0 |\n+----------+-----+-----+-----+-----+-----+-----+\n| 6.0_C    | 0.0 | 0.5 | 0.5 | 0.0 | 0.0 | 0.0 |\n+----------+-----+-----+-----+-----+-----+-----+\n| 7.0_G    | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 |\n+----------+-----+-----+-----+-----+-----+-----+\n| 8.0_T    | 0.0 | 0.0 | 0.0 | 0.5 | 0.0 | 0.5 |\n+----------+-----+-----+-----+-----+-----+-----+\n\nFrequencies of non-canonical (ambiguous) nucleotides are by default squashed into the ``oth``\ncolumn, but they can also be shown separately using a simple flag.\n\nallfreqs can be used either as a command line tool or through its Python API.\n\nFor more information, please refer to the Usage_ section of the documentation.\n\nInstallation\n============\n\n**PLEASE NOTE: allfreqs only supports Python \u003e= 3.6!**\n\nThe preferred installation method for allfreqs is using ``pip``:\n\n.. code-block:: console\n\n    $ pip install allfreqs\n\nFor more information, please refer to the Installation_ section of the documentation.\n\nCredits\n=======\n\nThis package was created with Cookiecutter_ and the 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