EMBOSS: fdrawtree

fdrawtree

Wiki

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Function

Plots an unrooted tree diagram

Description

Plots unrooted phylogenies, cladograms, circular trees and phenograms in a wide variety of user-controllable formats. The program is interactive and allows previewing of the tree on PC, Macintosh, or X Windows screens, or on Tektronix or Digital graphics terminals. Final output can be to a file formatted for one of the drawing programs, for a ray-tracing or VRML browser, or one at can be sent to a laser printer (such as Postscript or PCL-compatible printers), on graphics screens or terminals, on pen plotters or on dot matrix printers capable of graphics.

Similar to DRAWGRAM but plots unrooted phylogenies.

Algorithm

DRAWTREE interactively plots an unrooted tree diagram, with many options including orientation of tree and branches, label sizes and angles, margin sizes. Particularly if you can use your computer screen to preview the plot, you can very effectively adjust the details of the plotting to get just the kind of plot you want.

To understand the working of DRAWGRAM and DRAWTREE, you should first read the Tree Drawing Programs web page in this documentation.

As with DRAWGRAM, to run DRAWTREE you need a compiled copy of the program, a font file, and a tree file. The tree file has a default name of intree. The font file has a default name of "fontfile". If there is no file of that name, the program will ask you for the name of a font file (we provide ones that have the names font1 through font6). Once you decide on a favorite one of these, you could make a copy of it and call it fontfile, and it will then be used by default. Note that the program will get confused if the input tree file has the number of trees on the first line of the file, so that number may have to be removed.

Usage

Here is a sample session with fdrawtree

% fdrawtree -previewer n Plots an unrooted tree diagram Phylip tree file: drawgram.tree Phylip drawtree output file [drawgram.fdrawtree]: DRAWTREE from PHYLIP version 3.69 Reading tree ... Tree has been read. Loading the font ... Font loaded. Writing plot file ... Plot written to file "drawgram.fdrawtree" Done.

Go to the input files for this example
Go to the output files for this example

Command line arguments

Plots an unrooted tree diagram
Version: EMBOSS:6.2.0

   Standard (Mandatory) qualifiers:
  [-intreefile]        tree       Phylip tree file
  [-plotfile]          outfile    [*.fdrawtree] Phylip drawtree output file

   Additional (Optional) qualifiers (* if not always prompted):
   -plotter            menu       [l] Plotter or printer the tree will be
                                  drawn on (Values: l (Postscript printer file
                                  format); m (PICT format (for drawing
                                  programs)); j (HP Laserjet 75 dpi PCL file
                                  format); s (HP Laserjet 150 dpi PCL file
                                  format); y (HP Laserjet 300 dpi PCL file
                                  format); w (MS-Windows Bitmap); f (FIG 2.0
                                  drawing program format); a (Idraw drawing
                                  program format); z (VRML Virtual Reality
                                  Markup Language file); n (PCX 640x350 file
                                  format (for drawing programs)); p (PCX
                                  800x600 file format (for drawing programs));
                                  q (PCX 1024x768 file format (for drawing
                                  programs)); k (TeKtronix 4010 graphics
                                  terminal); x (X Bitmap format); v (POVRAY 3D
                                  rendering program file); r (Rayshade 3D
                                  rendering program file); h (Hewlett-Packard
                                  pen plotter (HPGL file format)); d (DEC
                                  ReGIS graphics (VT240 terminal)); e (Epson
                                  MX-80 dot-matrix printer); c
                                  (Prowriter/Imagewriter dot-matrix printer);
                                  t (Toshiba 24-pin dot-matrix printer); o
                                  (Okidata dot-matrix printer); b (Houston
                                  Instruments plotter); u (other (one you have
                                  inserted code for)))
   -previewer          menu       [x] Previewing device (Values: n (Will not
                                  be previewed); I i (MSDOS graphics screen
                                  m:Macintosh screens); x (X Windows display);
                                  w (MS Windows display); k (TeKtronix 4010
                                  graphics terminal); d (DEC ReGIS graphics
                                  (VT240 terminal)); o (Other (one you have
                                  inserted code for)))
   -iterate            menu       [e] Iterate to improve tree (Values: n (No);
                                  e (Equal-Daylight algorithm); b (n-Body
                                  algorithm))
   -lengths            boolean    [N] Use branch lengths from user trees
   -labeldirection     menu       [m] Label direction (Values: a (along); f
                                  (fixed); r (radial); m (middle))
   -treeangle          float      [90.0] Angle the tree is to be plotted
                                  (Number from -360.000 to 360.000)
   -arc                float      [360] Degrees the arc should occupy (Number
                                  from 0.000 to 360.000)
*  -labelrotation      float      [90.0] Angle of labels (0 degrees is
                                  horizontal for a tree growing vertically)
                                  (Number from 0.000 to 360.000)
   -[no]rescaled       toggle     [Y] Automatically rescale branch lengths
*  -bscale             float      [1.0] Centimeters per unit branch length
                                  (Any numeric value)
   -treedepth          float      [0.53] Depth of tree as fraction of its
                                  breadth (Number from 0.100 to 100.000)
*  -xmargin            float      [1.65] Horizontal margin (cm) (Number 0.100
                                  or more)
*  -ymargin            float      [2.16] Vertical margin (cm) (Number 0.100 or
                                  more)
*  -xrayshade          float      [1.65] Horizontal margin (pixels) (Number
                                  0.100 or more)
*  -yrayshade          float      [2.16] Vertical margin (pixels) (Number
                                  0.100 or more)
   -paperx             float      [20.63750] Paper width (Any numeric value)
   -papery             float      [26.98750] Paper height (Number 0.100 or
                                  more)
   -pagesheight        float      [1] Number of trees across height of page
                                  (Number 1.000 or more)
   -pageswidth         float      [1] Number of trees across width of page
                                  (Number 1.000 or more)
   -hpmargin           float      [0.41275] Horizontal overlap (cm) (Number
                                  0.001 or more)
   -vpmargin           float      [0.53975] Vertical overlap (cm) (Number
                                  0.001 or more)

   Advanced (Unprompted) qualifiers:
   -fontfile           string     [font1] Fontfile name (Any string)

   Associated qualifiers:

   "-plotfile" associated qualifiers
   -odirectory2        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

Qualifier Type Description Allowed values Default

Standard (Mandatory) qualifiers

[-intreefile]
(Parameter 1) tree Phylip tree file Phylogenetic tree

[-plotfile]
(Parameter 2) outfile Phylip drawtree output file Output file <*>.fdrawtree

Additional (Optional) qualifiers

-plotter list Plotter or printer the tree will be drawn on
l (Postscript printer file format)
m (PICT format (for drawing programs))
j (HP Laserjet 75 dpi PCL file format)
s (HP Laserjet 150 dpi PCL file format)
y (HP Laserjet 300 dpi PCL file format)
w (MS-Windows Bitmap)
f (FIG 2.0 drawing program format)
a (Idraw drawing program format)
z (VRML Virtual Reality Markup Language file)
n (PCX 640x350 file format (for drawing programs))
p (PCX 800x600 file format (for drawing programs))
q (PCX 1024x768 file format (for drawing programs))
k (TeKtronix 4010 graphics terminal)
x (X Bitmap format)
v (POVRAY 3D rendering program file)
r (Rayshade 3D rendering program file)
h (Hewlett-Packard pen plotter (HPGL file format))
d (DEC ReGIS graphics (VT240 terminal))
e (Epson MX-80 dot-matrix printer)
c (Prowriter/Imagewriter dot-matrix printer)
t (Toshiba 24-pin dot-matrix printer)
o (Okidata dot-matrix printer)
b (Houston Instruments plotter)
u (other (one you have inserted code for))
l

-previewer list Previewing device
n (Will not be previewed)
I i (MSDOS graphics screen m:Macintosh screens)
x (X Windows display)
w (MS Windows display)
k (TeKtronix 4010 graphics terminal)
d (DEC ReGIS graphics (VT240 terminal))
o (Other (one you have inserted code for))
x

-iterate list Iterate to improve tree
n (No)
e (Equal-Daylight algorithm)
b (n-Body algorithm)
e

-lengths boolean Use branch lengths from user trees Boolean value Yes/No No

-labeldirection list Label direction
a (along)
f (fixed)
r (radial)
m (middle)
m

-treeangle float Angle the tree is to be plotted Number from -360.000 to 360.000 90.0

-arc float Degrees the arc should occupy Number from 0.000 to 360.000 360

-labelrotation float Angle of labels (0 degrees is horizontal for a tree growing vertically) Number from 0.000 to 360.000 90.0

-[no]rescaled toggle Automatically rescale branch lengths Toggle value Yes/No Yes

-bscale float Centimeters per unit branch length Any numeric value 1.0

-treedepth float Depth of tree as fraction of its breadth Number from 0.100 to 100.000 0.53

-xmargin float Horizontal margin (cm) Number 0.100 or more 1.65

-ymargin float Vertical margin (cm) Number 0.100 or more 2.16

-xrayshade float Horizontal margin (pixels) Number 0.100 or more 1.65

-yrayshade float Vertical margin (pixels) Number 0.100 or more 2.16

-paperx float Paper width Any numeric value 20.63750

-papery float Paper height Number 0.100 or more 26.98750

-pagesheight float Number of trees across height of page Number 1.000 or more 1

-pageswidth float Number of trees across width of page Number 1.000 or more 1

-hpmargin float Horizontal overlap (cm) Number 0.001 or more 0.41275

-vpmargin float Vertical overlap (cm) Number 0.001 or more 0.53975

Advanced (Unprompted) qualifiers

-fontfile string Fontfile name Any string font1

Associated qualifiers

"-plotfile" associated outfile qualifiers

-odirectory2
-odirectory_plotfile string Output directory Any string

General qualifiers

-auto boolean Turn off prompts Boolean value Yes/No N

-stdout boolean Write first file to standard output Boolean value Yes/No N

-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N

-options boolean Prompt for standard and additional values Boolean value Yes/No N

-debug boolean Write debug output to program.dbg Boolean value Yes/No N

-verbose boolean Report some/full command line options Boolean value Yes/No Y

-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N

-warning boolean Report warnings Boolean value Yes/No Y

-error boolean Report errors Boolean value Yes/No Y

-fatal boolean Report fatal errors Boolean value Yes/No Y

-die boolean Report dying program messages Boolean value Yes/No Y

-version boolean Report version number and exit Boolean value Yes/No N

Input file format

fdrawtree input ...

Input files for usage example

File: drawgram.tree

(Delta,(Epsilon,(Gamma,(Beta,Alpha))));

Output file format

fdrawtree outputs ...

Output files for usage example

Graphics File: drawgram.fdrawtree

[fdrawtree results]

Data files

The font file has a default name of "fontfile". If there is no file of that name, the program will ask you for the name of a font file (we provide ones that have the names font1 through font6). Once you decide on a favorite one of these, you could make a copy of it and call it fontfile, and it will then be used by default.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

Program name	Description
fdrawgram	Plots a cladogram- or phenogram-like rooted tree diagram
fretree	Interactive tree rearrangement

Author(s)

This program is an EMBOSS conversion of a program written by Joe Felsenstein as part of his PHYLIP package.

Although we take every care to ensure that the results of the EMBOSS version are identical to those from the original package, we recommend that you check your inputs give the same results in both versions before publication.

Please report all bugs in the EMBOSS version to the EMBOSS bug team, not to the original author.

History

Written (2004) - Joe Felsenstein, University of Washington.

Converted (August 2004) to an EMBASSY program by the EMBOSS team.

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Wiki

Function

Description

Algorithm

Usage

Command line arguments

Input file format

Input files for usage example

File: drawgram.tree

Output file format

Output files for usage example

Graphics File: drawgram.fdrawtree

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users