Man page - pxbp(1)

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Package: phyx
apt-get install phyx

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phyx

Manual

PXBP

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
CITATION
AUTHOR
REPORTING BUGS
COPYRIGHT

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>