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        "author": "Janina Mass",
        "author_email": "janina.mass@hhu.de",
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        "description": "===========\nPysickle\n===========\n\n**pysickle.py** will try to remove sequences that cause misalignments from a multiple sequence alignment (MSA). It reads a given MSA in multi-fasta format and removes sequences with the highest penalty scores, then builds the next MSA without those sequences. This process is repeated until a user-specified cuttoff is reached or less than three sequences are left to be aligned.\n\nUsage::\n\n    ######################################\n    # pysickle.py\n    ######################################\n    usage:\n        pysickle.py -f multifasta alignment\n    options:\n        -f, --fasta=FILE    multifasta alignment (eg \"align.fas\")\n        OR\n        -F, --fasta_dir=DIR directory with multifasta files (needs -s SUFFIX)\n        -s, --suffix=SUFFIX will try to work with files that end with SUFFIX\n                            (eg \".fas\")\n\n        -a, --msa_tool=STR  supported: \"mafft\" [default:\"mafft\"]\n        -i, --max_iterations=NUM    force stop after NUM iterations\n        -n, --num_threads=NUM   max number of threads to be executed in \n                                parallel [default: 1]\n\n        -h, --help      prints this\n\n\nCurrently supported multiple sequence aligners:\n\n- mafft (Katoh, Standley 2013 (Molecular Biology and Evolution 30:772-780) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. http://mafft.cbrc.jp/alignment/software/)\n\n\nRequirements\n============\n* matplotlib\n* numpy\n\nExternal Programs\n-----------------\n* mafft",
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