PhyloTerraces Files

INFORMATION FOR TERRACE VISUALIZATION CODE (Sanderson et al., in prep.)

Software written 2011, by Mike Sanderson

Draws a 3-D rendering of terraces in phylogenetic tree space, in which the size of each 
terrace is proportional to the number of trees on the terrace, and the height is proportional
to the likelihood score.

USAGE: tree_space -f inputfile

The format of the input file is two columns, tab delimited, with one terrace per row. The first field
has the likelihood (or other) score, the second has the number of trees on the terrace. A sample file,
'TerraceTable169' is provided, which matches the figure in the paper.


COMPILATION: Source code in C is provided, along with a Makefile for MacOS X. It should be straightforward
to port to other systems having an OpenGL library.

On the Mac, from a terminal window, move to the directory containing the untarred and uncompressed source files
and type 

	make -f makefile.macosx

You may need to have gcc (as part of the Apple Developer's Kit) installed. For questions, consult your local unixhead.

USING THE PROGRAM: The program is based on code developed for my 'paloverde' tree viz software, which you
might want to consult for a full list of many of the features. Short of that, note that the orientation of the object
and distance to the viewpoint can be controlled by left-clicking and moving the mouse, and shift-left-clicking and moving
the mouse, respectively. Arrow keys also work, with and without the shift button. 

Every aspect of color, lighting, etc., can be modified by monkeying with the openGL in the file tree_openGL.c.


PRINTING: Well, good luck. It's openGL, after all. Two solutions: 1) take a screen shot with 'grab' and go from there,
or 2) set the variable TILES to 1 in the file tree_openGL.c and recompile. On running, this makes a very large file called
tileimg.ppm file with a high resolution image. You can convert to PDF or other stuff with something like imagemagick.