pxbp1
Print out bipartitions found in treefiles
Usage
pxbp [OPTIONS] ...
Overview
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.
Releases
3 releases since Debian 10 (Buster); the text changed 2 times.
--citation since Debian 12 (Bookworm);
--cutoff since Debian 12 (Bookworm);
--edgeall since Debian 12 (Bookworm);
--maptree since Debian 12 (Bookworm);
--suppress since Debian 12 (Bookworm);
--uniquetree since Debian 12 (Bookworm);
--verbose since Debian 12 (Bookworm);
-C since Debian 12 (Bookworm);
-c since Debian 12 (Bookworm);
-e since Debian 12 (Bookworm);
-m since Debian 12 (Bookworm);
-s since Debian 12 (Bookworm);
-u since Debian 12 (Bookworm);
-v since Debian 12 (Bookworm).