Large Scale Phylogenetic Rendering

The New York Times is running an article, "Crunching the Data for the Tree of Life":

For years now researchers have sequenced DNA from thousands of species from jungles, tundras and museum drawers. They have used supercomputers to crunch the genetic data and have gleaned clues to how today ’s diversity of species evolved over the past 450 million years. There’s just one problem. They have no way to visualize it...

The article mainly concerns itself with large scale phylogenetic analysis and rendering. The kind of rendering you would do with ATV or PAUP is for small sub branches of the total tree of life. This article analogizes the goals of these programs with Google Earth, programs that can quickly deal with large scale data sets.

One of the programs mentioned is Paloverde program from UC Davis(The site mentioned in the paper seemd to be down, but you can find a Arizona mirror to download the program).  They provide a compiled binary for Mac OSX.

Another program for this type of large scale rendering is Phlyo3D that works in conjunction with Walrus, a Java3D based graph rendering platform.

GCC compiler directives

When ever you start coding on separate platforms, you need to start
thinking about compiler directives.   That way, you can write
separate code for different needs. Follow the break to find out how to take advantage of GCC compiler directives.



To get the list of directives
from gcc use the command

echo "" | gcc -E -dM -

Using this you can find the gcc for linux and MacOS have the directive
'__linux' and '__APPLE__'

An example of how I use this info is my OpenGL header file requests.

#if __linux
#define  GL_GLEXT_PROTOTYPES
#include <GL/gl.h>
#include <GL/glu.h>
#include <GL/glext.h>
#include <GL/glut.h>
#else
#if __APPLE__
#include <opengl/gl.h>
#include <opengl/glu.h>
#include <glut/glut.h>
#endif
#endif

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