parasail_aligner - Development heaaders and static libraries for parasail

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

parasail_aligner 2.4.1                             April 2020                                PARASAIL_ALIGNER(1)

       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'

       parasail_aligner - Development heaaders and static libraries for parasail