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njplot(1) [debian man page]

NJPLOT(1)						      General Commands Manual							 NJPLOT(1)

NAME
njplot - A phylogenetic tree drawing program for biologists newicktops - draw phylogenetic trees into PostScript file SYNOPSIS
njplot [options] tree_file newicktops [options] tree_file newicktotxt [options] tree_file DESCRIPTION
This manual page documents briefly the njplot command. The newicktops command does exactly the same but needs no X11 display. The output is rendered into a PostScript file. The newicktotxt command does exactly the same as newicktops but the output is rendered into a text file. This manual page was rewritten for the Debian GNU/Linux distribution because the original program does not have a manual page. njplot is a tree drawing program able to draw any binary or multi-branched tree expressed in the standard phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods. Any rooting of the unrooted tree can be interactively specified using the mouse. NJplot also allows zooming, branch swapping, display of bootstrap scores and saving in the PostScript format. NJplot can therefore be used as a graphical extension of any package of phylogenetic program which employs the standard tree format for storing trees (i.e., with most such packages). OPTIONS
There are only the following options which only work in an x-terminal-emulator, but not in console mode: -h Prints out brief help. -us Postscript tree file prepared for US Letter paper size. -psonly No window interface, just write the PostScript tree file. -size n Font size n used for taxon names. -pc n number of pages for PostScript output. -psize widthxheight size of PostScript page expressed as WIDTHxHEIGHT. -lengths Show branch lengths if they appear in tree file. -boot Show bootstrap values if they appear in tree file. -notitle Don't include title in PostScript output. SEE ALSO
unrooted(1). Word-Wide-Web: http://pbil.univ-lyon1.fr/software/njplot.html AUTHOR
: Manolo Gouy e-mail: mgouy@biomserv.univ-lyon1.fr This manual page was written by Dr. Guenter Bechly <gbechly@debian.org>, for the Debian GNU/Linux system (but may be used by others). April 10, 2001 NJPLOT(1)

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TGTT(1) 						      General Commands Manual							   TGTT(1)

NAME
tgtt - Tool for Generic Textual Trees SYNOPSIS
tgtt [options] [tree] DESCRIPTION
tgtt is an X11/Motif based graphical editor for drawing generic textual trees. Trees can be loaded from and stored to a file. It can print trees to a PostScript printer or save as PostScript to a file. tgtt is part of The Toolkit for Conceptual Modeling (TCM). ARGUMENTS
You can call tgtt with a single tree name as argument. If this argument is an existing file then tgtt tries to load a tree from it. If it does not exist, a new tree is created with the argument as tree name. tgtt files should have suffix '*.gtt'. Without a tree argument, tgtt creates a new empty generic tree with the name 'untitled.gtt'. In addition to the standard X11 toolkit options (see X11(7)) tgtt accepts the options listed below: -drawing widthxheight Create a drawing area of width pixels wide and height pixels high. -help Write all available options to standard output and quit. -maxdrawing widthxheight The drawing area can not be larger than width pixels wide and height pixels high. -priv_cmap Start the editor with a private colormap. -projdir directory Set the project directory (current working directory) to directory. -toEPS [file.eps] Generate EPS (to file.eps or stdout when no file name was given) and quit. -toFig [file.fig] [-latex] Generate Fig format (to file.fig or stdout when no file name was given and quit. When the -latex option is given, LaTeX fonts are generated, otherwise normal PostScript fonts are generated. The Fig format can be read by xfig(1) and fig2dev(1). -toPNG file.png Generate PNG format to file.png and quit. -toPS [file.ps] Generate PostScript (to file.ps or stdout when no file name was given) and quit. -version Write the TCM version to standard output and quit. ENVIRONMENT
The TCM_HOME environment variable should be the directory where the TCM files are installed. PATH Should include $TCM_HOME/bin MANPATH Should include $TCM_HOME/man PRINTER Name of the default printer that is used by tgtt. LD_LIBRARY_PATH Should include $TCM_HOME/lib when the distribution contains shared object libraries in $TCM_HOME/lib. FILES
The following relative files are relative to $TCM_HOME. bin/tgtt the generic textual tree editor. bin/psf a program to filter PostScript output. lib/banner.ps PostScript banner page that can be used when the printer does not print a banner page. lib/help/* The help directory contains a collection of text files for the on-line help. lib/TCM X Resources (the same as the ones that are built-in). You can customize the fonts and colors by setting resources in your X defaults database. Each string of the form ``TCM.resource:definition'' sets a resource. /tmp/tcmXXXXXX Pseudo random temporary file, for PostScript output. lib/tcm.conf TCM editor configuration file. This file contains values for some of the editor defaults like the page size, the default fonts etc. This file is read by each editor upon startup. $HOME/.tcmrc Each user of TCM can override some of the options of tcm.conf by its own configuration file, installed in $HOME/.tcmrc. SEE ALSO
Frank Dehne, Roel Wieringa and Henk van de Zandschulp -- TCM (Toolkit for Conceptual Modeling), User's Guide and Reference. This document is available as PostScript and HTML in $TCM_HOME/doc or as HTML via the URL http://www.cs.utwente.nl/~tcm/tcm-usersguide.html. tcm(1), X11(7), xfig(1), fig2dev(1) AUTHOR
Frank Dehne (frank@cs.vu.nl). BUGS
Please send bug reports to tcm@cs.utwente.nl. 9 January 2000 TGTT(1)
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