seqSieve 0.9.1

seqSieve 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 cutt-off is reached or less than three sequences are left to be aligned.

Usage:

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# seqSieve.py
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usage:
   seqSieve.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", prank, prankf (= prank +F) [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]
    -m, --mode=MODE         set strategy to remove outlier sequences [default: "Sites"]
                            available modes (not case sensitive):
                                "Sites", "Gaps", "uGaps","Insertions",
                                "uInsertions","uInsertionsGaps", "custom"
    -q, --no-realign        don't realign with each iteration (not recommended)
    -l, --log       write logfile
    -h, --help      prints this

only for mode "custom":
    -g, --gap_penalty=NUM        set gap penalty [default: 1.0]
    -G, --unique_gap_penalty=NUM set unique gap penalty [default: 10.0]
    -j, --insertion_penalty=NUM  set insertion penalty [default:1.0]
    -J, --unique_insertion_penalty=NUM set insertion penalty [default:1.0]
    -M, --mismatch_penalty=NUM   set mismatch penalty [default:1.0]
    -r, --match_reward=NUM       set match reward [default: -10.0]

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/)

• prank (Loytynoja, Goldman 2005 (PNAS 102:10557-10562) An algorithm for progressive multiple alignment of sequences with insertions. http://www.ebi.ac.uk/goldman-srv/prank/prank/