Man page - pxrr(1)

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Package: phyx
apt-get install phyx

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phyx

Manual

PXRR

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
CITATION
AUTHOR
REPORTING BUGS
COPYRIGHT

NAME

pxrr - reroot (or unroot) a tree file and produce a newick

SYNOPSIS

pxrr [ OPTIONS ]...

DESCRIPTION

Reroot (or unroot) a tree file and produce a newick. This will take a newick- or nexus-formatted tree from a file or STDIN. Output is written in newick format.

OPTIONS

-t , --treef = FILE

input tree file, STDIN otherwise

-g , --outgroups = CSL

outgroup sep by commas (NO SPACES!)

-f , --namesf = FILE

outgroups in a file (each on a line)

-r , --ranked

turn on ordering of outgroups. will root on first one present

-u , --unroot

unroot the tree

-s , --silent

do not error if outgroup(s) not found

-o , --outf = FILE

output tree 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), Joseph W. Brown

REPORTING BUGS

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