Provided by: phyx_1.3.1+ds-2_amd64
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>
COPYRIGHT
Copyright © 2013-2021 FePhyFoFum License GPLv3