Man page - pxnw(1)

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Package: phyx
apt-get install phyx

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phyx

Manual

PXNW

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
CITATION
AUTHOR
REPORTING BUGS
COPYRIGHT

NAME

pxnw - conduct Needleman-Wunsch analysis for all the seqs in a file

SYNOPSIS

pxnw [ OPTIONS ]...

DESCRIPTION

Conduct Needleman-Wunsch 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>