
                                 fdrawtree 



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 
Plots an unrooted tree diagram
Phylip tree file: drawgram.tree
Phylip drawtree output file [drawgram.fdrawtree]: 

DRAWTREE from PHYLIP version 3.6b
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

   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 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); p (PCX 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)))
*  -plotterpcl         menu       [1] Laserjet resolution (Values: 1 (75 DPI);
                                  2 (150 DPI); 3 (300 DPI))
*  -plotterpcx         menu       [1] PCX file resolution (Values: 1 (EGA 640
                                  X 350); 2 (VGA 800 X 600); 3 (VGA 1024 X
                                  768))
   -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)
*  -xmarginray         float      [1.65] Horizontal margin (pixels) (Number
                                  0.100 or more)
*  -ymarginray         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     Fontfile name (Any string is accepted)

   Associated qualifiers:

   "-plotfile" associated qualifiers
   -odirectory2        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write 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. 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

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

  File: drawgram.fdrawtree

%!PS-Adobe-2.0
%%Title: Phylip Tree Output
%%DocumentFonts: (atend)
%%Pages: 1 1
%%BoundingBox: 0 0 612 792
%%DocumentPaperSizes: Letter
%%Orientation: Portrait
%%EndComments
/l {newpath moveto lineto stroke} def
%%EndProlog
%%
%%Page: 1 1
%%PageBoundingBox: 0 0 585 765
%%PageFonts: (atend)
%%BeginPageSetup
%%PaperSize: Letter
 1 setlinecap
 1 setlinejoin
    4.25 setlinewidth newpath
%!PS-Adobe-2.0
%%Title: Phylip Tree Output
%%DocumentFonts: (atend)
%%Pages: 1 1
%%BoundingBox: 0 0 612 792
%%DocumentPaperSizes: Letter
%%Orientation: Portrait
%%EndComments
/l {newpath moveto lineto stroke} def
%%EndProlog
%%
%%Page: 1 1
%%PageBoundingBox: 0 0 585 765
%%PageFonts: (atend)
%%BeginPageSetup
%%PaperSize: Letter
 1 setlinecap
 1 setlinejoin
    4.72 setlinewidth newpath
  193.10   333.75   147.15   270.50 l
  193.10   333.75   239.05   396.99 l
  239.05   396.99   179.40   447.52 l
  239.05   396.99   315.51   413.26 l
  315.51   413.26   330.54   489.97 l
  315.51   413.26   377.62   365.78 l
  377.62   365.78   450.44   394.22 l
  377.62   365.78   406.77   293.25 l
 stroke    1.57 setlinewidth
1 setlinecap 1 setlinejoin
gsave
/Times-Roman findfont 39.641216 scalefont setfont
104.222223 231.138753 translate 0.000000 rotate
0 0 moveto
(Delta) show
grestore
gsave
/Times-Roman findfont 39.641216 scalefont setfont
118.832100 460.640405 translate 0.000000 rotate
0 0 moveto
(Epsilon) show
grestore
gsave
/Times-Roman findfont 39.641216 scalefont setfont
267.784752 503.095985 translate 0.000000 rotate
0 0 moveto
(Gamma) show
grestore
gsave
/Times-Roman findfont 39.641216 scalefont setfont
463.561935 400.403476 translate 0.000000 rotate
0 0 moveto
(Beta) show
grestore
gsave
/Times-Roman findfont 39.641216 scalefont setfont
358.330872 253.884183 translate 0.000000 rotate
0 0 moveto
(Alpha) show
grestore
stroke     4.72 setlinewidth
 1 setlinecap 1 setlinejoin
stroke showpage

%%PageTrailer
%%PageFonts: Times-Roman
%%Trailer
%%DocumentFonts: Times-Roman

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
   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.
