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PXSW(1) User Commands PXSW(1)

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.
May 2018 pxsw 0.99+ds