Gangolf Jobb gangolf at TREEFINDER.DE
Thu Nov 18 10:51:16 CST 2004

Here is the new world's fastest maximum likelihood phylogeny program on a PC:

TREEFINDER has a new tree search algorithm. In my simulations, the new
TREEFINDER is three times faster than PHYML, which is the second fastest
program. The results are in the manual.

Tree calibration has been extended. Now, TREEFINDER supports multiple
calibration points and time intervals. One can specify time boundaries for
tips as well as for internal nodes in a tree. I have invented and added two
new flavours of rate smoothing to overcome some problems with Sanderson's
NPRS: The Global Rate Minimum Deformation method (GRMD), and the Local Rate
Minimum Deformation method (LRMD).

I have also improved the utility to check for compositional equilibrium in a
sequence alignment. In addition to computing p-values for individual
sequences, the tool now visualizes the distribution of base frequencies over
sites as well as over species.

Maximum likelihood optimization under the molecular clock is no longer
supported. In my opinion, the underlying assumtion of a constant rate is
unrealistic and not really worth the huge effort on the algorithmic side.
For calibration purposes, rate smoothing can achieve the same much easier
and has the merit of distinguishing clearly between the time scale and the
distance scale. Moreover, one can incorporate explicit assumptions about the
rate evolution into the objective function. If you feel that my opinion is
wrong, you may try convincing me to re-implement the clock constraint in a
future release.

As usual, the program is available for Windows, Linux, MacOS X and Solaris.

Did you know that a German scientist earns less than a worker in car
industry, but has studied for years? Obviously, cars are much more useful
than most of science. Please note, that I am currently not being paid for my
work. I am looking for a position in Munich, where I can continue the


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