NAME

       pxsw - Conduct Smith-Waterman analysis for all the seqs in a file.

SYNOPSIS

       pxsw [OPTION]... [FILE]...

DESCRIPTION

       Conduct  Smith-Waterman analysis for all the seqs in a file.  This will take fasta, fastq,
       phylip, and nexus inputs.  Output  is  a  list  of  the  scores  and  distances  (and  the
       alignments if asked).  Can read from stdin or file.

       -s, --seqf=FILE
              input sequence file, stdin otherwise

       -o, --outf=FILE
              output score/distance file, stout otherwise

       -a, --outalnf=FILE
              output sequence file, won't output otherwise

       -t, --seqtype=INT
              sequence type, default=DNA (DNA=0,AA=1)

       -m, --matrix=FILE
              scoring matrix, default DNA=EDNAFULL, AA=BLOSUM62

       -n, --nthreads=INT
              number of threads (open mp), default=2

       -v, --verbose
              make the output more verbose, turns off parallel

       -h, --help
              display this help and exit

       -V, --version
              display version and exit

REPORTING BUGS

       Report    bugs    to:    <https://github.com/FePhyFoFum/phyx/issues>   phyx   home   page:
       <https://github.com/FePhyFoFum/phyx>

AUTHOR

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