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.