.\" Automatically generated by Pandoc 3.0.1
.\"
.\" Define V font for inline verbatim, using C font in formats
.\" that render this, and otherwise B font.
.ie "\f[CB]x\f[]"x" \{\
. ftr V B
. ftr VI BI
. ftr VB B
. ftr VBI BI
.\}
.el \{\
. ftr V CR
. ftr VI CI
. ftr VB CB
. ftr VBI CBI
.\}
.TH "tree-tool" "1" "Feb 2018" "" ""
.hy
.SH NAME
.PP
\f[B]tree-tool\f[R] - Perform various operations on Newick trees.
.SH SYNOPSIS
.PP
\f[B]tree-tool\f[R] \f[I]tree-file\f[R] [OPTIONS]
.SH DESCRIPTION
.PP
Perform various operations on Newick trees.
.SH GENERAL OPTIONS:
.TP
\f[B]-h\f[R], \f[B]\[en]help\f[R]
produce help message
.TP
\f[B]-V\f[R], \f[B]\[en]verbose\f[R]
Output more log messages on stderr.
.SH MODIFICATION OPTIONS:
.TP
\f[B]\[en]prune\f[R] \f[I]arg\f[R]
Comma-separated taxa to remove
.TP
\f[B]\[en]resolve\f[R]
Comma-separated taxa to remove
.TP
\f[B]\[en]remove-root-branch\f[R]
Remove single branch from root.
.TP
\f[B]\[en]remove-root-branches\f[R]
Ensure root is not a tip.
.TP
\f[B]\[en]remove-knuckles\f[R]
Remove degree-2 nodes.
.TP
\f[B]\[en]scale\f[R] \f[I]arg\f[R]
Scale branch-lengths by factor
.TP
\f[B]\[en]strip-internal-names\f[R]
Remove internal node names
.TP
\f[B]\[en]name-all-nodes\f[R]
Add node names
.SH OUTPUT OPTIONS:
.TP
\f[B]\[en]length\f[R]
Report the total tree length
.TP
\f[B]\[en]diameter\f[R]
Report the total tree length
.SH REPORTING BUGS:
.PP
BAli-Phy online help: <http://www.bali-phy.org/docs.php>.
.PP
Please send bug reports to <bali-phy-users@googlegroups.com>.
.SH AUTHORS
Benjamin Redelings.