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fdrawtree |
Similar to DRAWGRAM but plots unrooted phylogenies.
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.
% fdrawtree Plots an unrooted tree diagram Input tree file: drawgram.tree 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
Standard (Mandatory) qualifiers: [-intreefile] tree (no help text) tree value [-plotfile] outfile Output file name Additional (Optional) qualifiers (* if not always prompted): -plotter menu Plotter or printer the tree will be drawn on * -plotterpcl menu Laserjet resolution * -plotterpcx menu PCX file resolution -previewer menu Previewing device -iterate menu Iterate to improve tree -lengths boolean Use branch lengths from user trees -labeldirection menu Label direction -treeangle float Angle the tree is to be plotted -arc float Degrees the arc should occupy * -labelrotation float Angle of labels (0 degrees is horizontal for a tree growing vertically) -[no]rescaled toggle Automatically rescale branch lengths * -bscale float Centimeters per unit branch length -treedepth float Depth of tree as fraction of its breadth * -xmargin float Horizontal margin (cm) * -ymargin float Vertical margin (cm) * -xmarginray float Horizontal margin (pixels) * -ymarginray float Vertical margin (pixels) -paperx float Paper width -papery float Paper height -pagesheight float Number of trees across height of page -pageswidth float Number of trees across width of page -hpmargin float Horizontal overlap (cm) -vpmargin float Vertical overlap (cm) Advanced (Unprompted) qualifiers: -fontfile string Fontfile 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 deaths |
Standard (Mandatory) qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||||||
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[-intreefile] (Parameter 1) |
(no help text) tree value | Phylogenetic tree | |||||||||||||||||||||||||||||||||||||||||
[-plotfile] (Parameter 2) |
Output file name | Output file | <sequence>.fdrawtree | ||||||||||||||||||||||||||||||||||||||||
Additional (Optional) qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||||||
-plotter | Plotter or printer the tree will be drawn on |
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l | ||||||||||||||||||||||||||||||||||||||||
-plotterpcl | Laserjet resolution |
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1 | ||||||||||||||||||||||||||||||||||||||||
-plotterpcx | PCX file resolution |
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1 | ||||||||||||||||||||||||||||||||||||||||
-previewer | Previewing device |
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x | ||||||||||||||||||||||||||||||||||||||||
-iterate | Iterate to improve tree |
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e | ||||||||||||||||||||||||||||||||||||||||
-lengths | Use branch lengths from user trees | Boolean value Yes/No | No | ||||||||||||||||||||||||||||||||||||||||
-labeldirection | Label direction |
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m | ||||||||||||||||||||||||||||||||||||||||
-treeangle | Angle the tree is to be plotted | Number from -360.000 to 360.000 | 90.0 | ||||||||||||||||||||||||||||||||||||||||
-arc | Degrees the arc should occupy | Number from 0.000 to 360.000 | 360 | ||||||||||||||||||||||||||||||||||||||||
-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 | ||||||||||||||||||||||||||||||||||||||||
-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 | Any string is accepted | An empty string is accepted |
(Delta,(Epsilon,(Gamma,(Beta,Alpha)))); |
%!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 |
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 |
---|---|
fdrawgram | Plots a cladogram- or phenogram-like rooted 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.