NAME

pxsw - manual page for pxsw 1.3

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

July 2021

pxsw 1.3