.\" Automatically generated by Pandoc 2.9.2.1
.\"
.TH "draw-tree" "1" "Feb 2018" "" ""
.hy
.SH NAME
.PP
\f[B]draw-tree\f[R] - Draw NEWICK (and some other) formatted files.
.SH SYNOPSIS
.PP
\f[B]draw-tree\f[R] [OPTIONS] \f[I]tree file\f[R]
.SH DESCRIPTION
.PP
Draw NEWICK (and some other) formatted files.
.SH INPUT OPTIONS:
.TP
\f[B]-h\f[R], \f[B]--help\f[R]
Produce help message
.TP
\f[B]-W\f[R] \f[I]arg\f[R] (=8.5), \f[B]--width\f[R] \f[I]arg\f[R] (=8.5)
Page width in inches
.TP
\f[B]-H\f[R] \f[I]arg\f[R] (=11), \f[B]--height\f[R] \f[I]arg\f[R] (=11)
Page height in inches
.TP
\f[B]--file\f[R] \f[I]arg\f[R]
predicates to examine
.TP
\f[B]--output\f[R] \f[I]arg\f[R] (=pdf)
Type of output to write: tree, topology, mtree, lengths, dot, ps, pdf,
svg
.TP
\f[B]--out\f[R] \f[I]arg\f[R]
Output filename (without extension)
.TP
\f[B]--full\f[R]
Consider only full splits by collapsing any partial splits.
.TP
\f[B]--iterations\f[R] \f[I]arg\f[R] (=2)
Number of iterations for layout algorithm
.TP
\f[B]--font-size\f[R] \f[I]arg\f[R] (=10)
Font size for taxon names
.TP
\f[B]--angle_iterations\f[R] \f[I]arg\f[R] (=0)
Number of iterations for layout algorithm with small-angle penalties
.TP
\f[B]--labels\f[R] \f[I]arg\f[R] (=horizontal)
Are the names horizontal or angled?
.TP
\f[B]--collapse\f[R]
Give node lengths evenly to neighboring branches and zero the node
lengths.
.TP
\f[B]--layout\f[R] \f[I]arg\f[R] (=graph)
Layout method: graph, equal-angle, equal-daylight, etc.
.TP
\f[B]--greedy\f[R]
For equal-daylight layout: take as much daylight as possible?
.TP
\f[B]--tree-layout-initial\f[R]
Start an energy layout with positions from the equal-angle layout - only
for multifurcating trees
.TP
\f[B]--no-shade\f[R]
For equal-daylight layout: reject rotations that shade other groups?
.TP
\f[B]--draw-clouds\f[R] \f[I]arg\f[R]
Draw wandering-ranges in MC trees as clouds.
.TP
\f[B]--seed\f[R] \f[I]arg\f[R]
Random seed
.TP
\f[B]--verbose\f[R]
Output more log messages on stderr.
.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.