NAME¶

pxmrcacut - extract subclades from trees

SYNOPSIS¶

pxmrcacut [OPTIONS]...

DESCRIPTION¶

Extract subclade(s) from tree(s). This will take a newick- or nexus-formatted tree from a file or STDIN, and an MRCA file with format: MRCANAME = tip1 tip2 ... If multiple MRCAs are provided, multiple subtrees are returned

OPTIONS¶

-t, --treef=FILE

input newick tree file, STDIN otherwise

-m, --mrca=FILE

file containing MRCA declarations

-o, --outf=FILE

output newick 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>

COPYRIGHT¶

Copyright © 2013-2021 FePhyFoFum License GPLv3