pxsw1

Usage

Overview

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.