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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.
Standard (Mandatory) qualifiers: [-fontfile] infile Fontfile [-intreefile] tree (no help text) tree value [-plotfile] outfile Output file name Additional (Optional) qualifiers (* if not always prompted): -[no]grows boolean Tree grows horizontally -style menu Tree style output -plotter menu Plotter or printer the tree will be drawn on -previewer menu Previewing device -lengths boolean Use branch lengths from user trees * -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 -stemlength float Stem length as fraction of tree depth -nodespace float Character height as fraction of tip spacing -nodeposition menu Position of interior nodes * -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: (none) Associated qualifiers: "-plotfile" associated qualifiers -odirectory3 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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[-fontfile] (Parameter 1) |
Fontfile | Input file | Required | ||||||||||||||||||||||||||||||||||||||||||||||||
[-intreefile] (Parameter 2) |
(no help text) tree value | Phylogenetic tree | |||||||||||||||||||||||||||||||||||||||||||||||||
[-plotfile] (Parameter 3) |
Output file name | Output file | <sequence>.fdrawgram | ||||||||||||||||||||||||||||||||||||||||||||||||
Additional (Optional) qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||||||||||||||
-[no]grows | Tree grows horizontally | Boolean value Yes/No | Yes | ||||||||||||||||||||||||||||||||||||||||||||||||
-style | Tree style output |
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c | ||||||||||||||||||||||||||||||||||||||||||||||||
-plotter | Plotter or printer the tree will be drawn on |
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l | ||||||||||||||||||||||||||||||||||||||||||||||||
-previewer | Previewing device |
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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 0.100 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 |
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||
(none) |
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 |
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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.