pxrmt1

Usage

Overview

Remove tree tips by label. 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

-n, --names=CSL

names sep by commas (NO SPACES!)

-f, --namesf=FILE

names in a file (each on a line)

-r, --regex=STRING

match tip labels by a regular expression

-c, --comp

take the complement (i.e. remove any taxa not in list)

-s, --silent

suppress warnings of missing tips

-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.