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.