Man page - pxrlt(1)

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Package: phyx
apt-get install phyx

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phyx

Manual

PXRLT

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
CITATION
AUTHOR
REPORTING BUGS
COPYRIGHT

NAME

pxrlt - taxon relabelling for trees

SYNOPSIS

pxrlt [ OPTIONS ]...

DESCRIPTION

Taxon relabelling for trees. Two ordered lists of taxa, -c (current) and -n (new) must be provided. Alternatively, a regex pattern ( -p ) and replacement ( -r ) text can be provided. 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

-c , --cnames = FILE

file containing current taxon labels (one per line)

-n , --nnames = FILE

file containing new taxon labels (one per line)

	-p , --pattern = STRING regex pattern to replace
	-r , --replace = STRING replacement pattern

-v , --verbose

make the output more verbose

-o , --outf = FILE

output 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 Joseph W. Brown, Stephen A. Smith (blackrim)

REPORTING BUGS

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