PXNW(1)

NAME
pxnw - Conduct Needleman-Wunsch analysis for all the seqs in a file.

SYNOPSIS
pxnw [OPTION]... [FILE]...

DESCRIPTION
Conduct Needleman-Wunsch analysis for all the seqs in a file. This will take fasta, fastq, phylip, and nexus inputs. Output is a list of the scores and distances (and the alignments if asked). Can read from stdin or file.

-s, --seqf=FILE
    input sequence file, stdin otherwise

-o, --outf=FILE
    output score/distance file, stout 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

-h, --help
    display this help and exit

-V, --version
    display version and exit

REPORTING BUGS
Report bugs to: <https://github.com/FePhyFoFum/phyx/issues> phyx home page: <https://github.com/FePhyFoFum/phyx>

AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.