NAME¶

pxbp - print out bipartitions found in treefiles

SYNOPSIS¶

pxbp [OPTIONS]...

DESCRIPTION¶

This will print out bipartitions found in treefile. Trees are assumed rooted unless the -e argument is provided. This will take a newick- or nexus-formatted tree from a file or STDIN.

OPTIONS¶

-t, --treef=FILE

input treefile, STDIN otherwise

-v, --verbose

give more output

-e, --edgeall

force edgewise (not node - so when things are unrooted) and assume all taxa are present in all trees

-u, --uniquetree

output unique trees and *no* other output

-m, --maptree=FILE

put the bipart freq on the edges of this tree. This will create a *.pxbpmapped.tre file.

-c, --cutoff

skip biparts that have support lower than this.

-s, --suppress

don't print all the output (maybe you use this with the maptree feature

-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 Stephen A. Smith (blackrim)

REPORTING BUGS¶

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

COPYRIGHT¶

Copyright © 2017-2024 FePhyFoFum License GPLv3