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