                                  fdrawgram



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Function

   Plots a cladogram- or phenogram-like rooted tree diagram

Description

   Plots rooted 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 DRAWTREE but plots rooted phylogenies.

Algorithm

   DRAWGRAM interactively plots a cladogram- or phenogram-like rooted tree
   diagram, with many options including orientation of tree and branches,
   style of tree, label sizes and angles, tree depth, margin sizes, stem
   lengths, and placement of nodes in the tree. Particularly if you can
   use your computer 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 DRAWTREE, to run DRAWGRAM 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 numbr may have to be
   removed.

Usage

   Here is a sample session with fdrawgram


% fdrawgram -previewer n
Plots a cladogram- or phenogram-like rooted tree diagram
Phylip tree file: drawgram.tree
Phylip drawgram output file [drawgram.fdrawgram]:

DRAWGRAM from PHYLIP version 3.69
Reading tree ...
Tree has been read.
Loading the font ....
Font loaded.

Writing plot file ...

Plot written to file "drawgram.fdrawgram"

Done.



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

Command line arguments

Plots a cladogram- or phenogram-like rooted tree diagram
Version: EMBOSS:6.2.0

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

   Additional (Optional) qualifiers (* if not always prompted):
   -[no]grows          boolean    [Y] Tree grows horizontally
   -style              menu       [c] Tree style output (Values: c (cladogram
                                  (v-shaped)); p (phenogram (branches are
                                  square)); v (curvogram (branches are 1/4 out
                                  of an ellipse)); e (eurogram (branches
                                  angle outward, then up)); s (swooporam
                                  (branches curve outward then reverse)); o
                                  (circular tree))
   -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 75 DPI Laserjet PCL file
                                  format); s (HP 150 DPI Laserjet PCL file
                                  format); y (HP 300 DPI Laserjet 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)))
   -lengths            boolean    [N] Use branch lengths from user trees
*  -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)
   -stemlength         float      [0.05] Stem length as fraction of tree depth
                                  (Number from 0.010 to 100.000)
   -nodespace          float      [0.3333] Character height as fraction of tip
                                  spacing (Number from 0.100 to 100.000)
   -nodeposition       menu       [c] Position of interior nodes (Values: i
                                  (Intermediate between their immediate
                                  descendants); w (Weighted average of tip
                                  positions); c (Centered among their ultimate
                                  descendants); n (Innermost of immediate
                                  descendants); v (So tree is v shaped))
*  -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) for
                                  Rayshade output (Number 0.100 or more)
*  -yrayshade          float      [2.16] Vertical margin (pixels) for Rayshade
                                  output (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


Input file format

   fdrawgram reads ...

  Input files for usage example

  File: drawgram.tree

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

Output file format

   fdrawgram output ...

  Output files for usage example

  Graphics File: drawgram.fdrawgram

   [fdrawgram 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.

See also

                    Program name          Description
                    fdrawtree    Plots an unrooted 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.
