NAME

       pxsw - conduct Smith-Waterman analysis for all seqs in a file

SYNOPSIS

       pxsw [OPTIONS]...

DESCRIPTION

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

OPTIONS

       -s, --seqf=FILE
              input sequence file, STDIN 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

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

       -h, --help
              display this help and exit

       -V, --version
              display version and exit

       -C, --citation
              display phyx citation and exit

CITATION

       Brown,  Joseph  W., Joseph F. Walker, and Stephen A. Smith. 2017. Phyx: phylogenetic tools
       for unix. Bioinformatics 33(12): 1886-1888. https://doi.org/10.1093/bioinformatics/btx063.

AUTHOR

       Written by Stephen A. Smith (blackrim)

REPORTING BUGS

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

COPYRIGHT

       Copyright © 2013-2021 FePhyFoFum License GPLv3