Pysickle

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.

Usage:

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# pysickle.py
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usage:
    pysickle.py -f multifasta alignment
options:
    -f, --fasta=FILE    multifasta alignment (eg "align.fas")
    OR
    -F, --fasta_dir=DIR directory with multifasta files (needs -s SUFFIX)
    -s, --suffix=SUFFIX will try to work with files that end with SUFFIX
                        (eg ".fas")

    -a, --msa_tool=STR  supported: "mafft" [default:"mafft"]
    -i, --max_iterations=NUM    force stop after NUM iterations
    -n, --num_threads=NUM   max number of threads to be executed in
                            parallel [default: 1]

    -h, --help      prints this

Currently supported multiple sequence aligners:

• 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/)