fdrawgram Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. 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 3.69.650 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:6.6.0.0 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. Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) 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. Comments None