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fdrawgram |
Similar to DRAWTREE but plots rooted phylogenies.
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.
% 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 3.67 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
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)
* -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 [font2] 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 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. 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
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| Standard (Mandatory) qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| [-intreefile] (Parameter 1) |
Phylip tree file | Phylogenetic tree | |||||||||||||||||||||||||||||||||||||||||||||||||
| [-plotfile] (Parameter 2) |
Phylip drawgram output file | Output file | <*>.fdrawgram | ||||||||||||||||||||||||||||||||||||||||||||||||
| Additional (Optional) qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||||||||||||||
| -[no]grows | Tree grows horizontally | Boolean value Yes/No | Yes | ||||||||||||||||||||||||||||||||||||||||||||||||
| -style | Tree style output |
|
c | ||||||||||||||||||||||||||||||||||||||||||||||||
| -plotter | Plotter or printer the tree will be drawn on |
|
l | ||||||||||||||||||||||||||||||||||||||||||||||||
| -previewer | Previewing device |
|
x | ||||||||||||||||||||||||||||||||||||||||||||||||
| -lengths | Use branch lengths from user trees | Boolean value Yes/No | No | ||||||||||||||||||||||||||||||||||||||||||||||||
| -labelrotation | Angle of labels (0 degrees is horizontal for a tree growing vertically) | Number from 0.000 to 360.000 | 90.0 | ||||||||||||||||||||||||||||||||||||||||||||||||
| -[no]rescaled | Automatically rescale branch lengths | Toggle value Yes/No | Yes | ||||||||||||||||||||||||||||||||||||||||||||||||
| -bscale | Centimeters per unit branch length | Any numeric value | 1.0 | ||||||||||||||||||||||||||||||||||||||||||||||||
| -treedepth | Depth of tree as fraction of its breadth | Number from 0.100 to 100.000 | 0.53 | ||||||||||||||||||||||||||||||||||||||||||||||||
| -stemlength | Stem length as fraction of tree depth | Number from 0.010 to 100.000 | 0.05 | ||||||||||||||||||||||||||||||||||||||||||||||||
| -nodespace | Character height as fraction of tip spacing | Number from 0.100 to 100.000 | 0.3333 | ||||||||||||||||||||||||||||||||||||||||||||||||
| -nodeposition | Position of interior nodes |
|
c | ||||||||||||||||||||||||||||||||||||||||||||||||
| -xmargin | Horizontal margin (cm) | Number 0.100 or more | 1.65 | ||||||||||||||||||||||||||||||||||||||||||||||||
| -ymargin | Vertical margin (cm) | Number 0.100 or more | 2.16 | ||||||||||||||||||||||||||||||||||||||||||||||||
| -xmarginray | Horizontal margin (pixels) | Number 0.100 or more | 1.65 | ||||||||||||||||||||||||||||||||||||||||||||||||
| -ymarginray | Vertical margin (pixels) | Number 0.100 or more | 2.16 | ||||||||||||||||||||||||||||||||||||||||||||||||
| -paperx | Paper width | Any numeric value | 20.63750 | ||||||||||||||||||||||||||||||||||||||||||||||||
| -papery | Paper height | Number 0.100 or more | 26.98750 | ||||||||||||||||||||||||||||||||||||||||||||||||
| -pagesheight | Number of trees across height of page | Number 1.000 or more | 1 | ||||||||||||||||||||||||||||||||||||||||||||||||
| -pageswidth | Number of trees across width of page | Number 1.000 or more | 1 | ||||||||||||||||||||||||||||||||||||||||||||||||
| -hpmargin | Horizontal overlap (cm) | Number 0.001 or more | 0.41275 | ||||||||||||||||||||||||||||||||||||||||||||||||
| -vpmargin | Vertical overlap (cm) | Number 0.001 or more | 0.53975 | ||||||||||||||||||||||||||||||||||||||||||||||||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||||||||||||||
| -fontfile | Fontfile name | Any string is accepted | font2 | ||||||||||||||||||||||||||||||||||||||||||||||||
(Delta,(Epsilon,(Gamma,(Beta,Alpha)))); |
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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.
| Program name | Description |
|---|---|
| fdrawtree | Plots an unrooted tree diagram |
| fretree | Interactive tree rearrangement |
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.
Converted (August 2004) to an EMBASSY program by the EMBOSS team.