Man page - pxsw(1)
Packages contas this manual
- pxtscale(1)
- pxs2fa(1)
- pxrecode(1)
- pxlstr(1)
- pxssort(1)
- pxrevcomp(1)
- pxrms(1)
- pxvcf2fa(1)
- pxmono(1)
- pxtrt(1)
- pxt2new(1)
- pxcolt(1)
- pxconsq(1)
- pxlog(1)
- pxrmt(1)
- pxboot(1)
- pxupgma(1)
- pxs2nex(1)
- pxfqfilt(1)
- pxtcomb(1)
- pxrlt(1)
- pxrr(1)
- pxmrcacut(1)
- pxmrca(1)
- pxrls(1)
- pxtcol(1)
- pxsstat(1)
- pxclsq(1)
- pxbdfit(1)
- pxmrcaname(1)
- pxnj(1)
- pxcltr(1)
- pxs2phy(1)
- pxcontrates(1)
- pxtlate(1)
- pxt2nex(1)
- pxbdsim(1)
- pxcomp(1)
- pxbp(1)
- pxpoly(1)
- pxstrec(1)
- pxnw(1)
- pxcat(1)
- pxsw(1)
- pxrmk(1)
- pxseqgen(1)
- pxtgen(1)
- pxlssq(1)
- pxaa2cdn(1)
Package: phyx
apt-get install phyx
apt-get install phyx
Manuals in package:
Documentations in package:
Manual
| PXSW(1) | User Commands | PXSW(1) |
NAME
pxsw - conduct Smith-Waterman analysis for all seqs in a file
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
Copyright © 2013-2024 FePhyFoFum License GPLv3
| June 2024 | pxsw 1.3.1 |