PARASAIL_ALIGNER(1)

NAME
parasail_aligner - Development heaaders and static libraries for parasail

DESCRIPTION
usage: parasail_aligner [-a funcname] [-c cutoff] [-x] [-e gap_extend] [-o gap_open] [-m matrix] [-t threads] [-d] [-M match] [-X mismatch] [-k band size (for nw_banded)] [-l AOL] [-s SIM] [-i OS] [-v] [-V] -f file [-q query_file] [-g output_file] [-O output_format {EMBOSS,SAM,SAMH,SSW}] [-b batch_size] [-r memory_budget] [-C] [-A alphabet_aliases]

  Defaults:

    funcname: sw_stats_striped_16

    cutoff: 7, must be >= 1, exact match length cutoff

    -x: if present, don't use suffix array filter

    gap_extend: 1, must be >= 0

    gap_open: 10, must be >= 0

    matrix: blosum62

    -d: if present, assume DNA alphabet ACGT

    match: 1, must be >= 0

    mismatch: 0, must be >= 0

    threads: system-specific default, must be >= 1

    AOL: 80, must be 0 <= AOL <= 100, percent alignment length SIM: 40, must be 0 <= SIM <= 100, percent exact matches

OS: 30, must be 0 <= OS <= 100, percent optimal score
    over self score

    -v: verbose output, report input parameters and timing -V: verbose memory output, report memory use

    file: no default, must be in FASTA format

    query_file: no default, must be in FASTA format

    output_file: parasail.csv

    output_format: no default, must be one of {EMBOSS,SAM,SAMH,SSW}

    batch_size: 0 (calculate based on memory budget),

    how many alignments before writing output

    memory_budget: 2GB or half available from system query (4.046 GB)

    -C: if present, use case sensitive alignments, matrices, etc.

alphabet_aliases: traceback will treat these pairs of characters as matches,

    for example, 'TU' for one pair, or multiple pairs as 'XYab'

AUTHOR
 This manpage was written by Nilesh Patra for the Debian distribution and
 can be used for any other usage of the program.