Software CLOCK-TREEFINDER

Gangolf Jobb jobb at STAT.UNI-MUENCHEN.DE
Tue Mar 23 07:11:16 CST 2004


A new TREEFINDER version is ready to download!

TREEFINDER can now optimize trees under a molecular clock. It searches for
optimal roots of clocklike trees, and thereby for the the most recent common
ancestor of a set of sequences. The new feature is also available in
bootstrap analysis, rate profiling and in all other utilities that involve
maximum likelihood tree reconstruction.

The other major improvement is a paired-sites test to estimate the
confidence of inferred branches, which is much faster than bootstrapping.
The so-called Local Rearrangement Paired-sites method (LRP) is following the
work of Kishino and Hasegawa (J. Mol. Evol. 29:170-179). By applying their
famous KH test to all local rearrangements in a tree, the LRP method is
assigning to every edge the probability that the local topology around the
edge has a higher likelihood than all near rearrangements.

The tree viewer has now a midpoint rooting utility and inferred trees come
midpoint-rooted by default. A codon position filter has been added to switch
on and off the codon positions in a sequence alignment. The frontend does
accept files by drag & drop, dialogs have been simplified. A help menu is
available.

Not new, but still worth mentioning is the fact that TREEFINDER is able to
compute trees from partially overlapping sequences.

Last but not least I managed to fix some problems with the Macintosh
frontend. The installing procedure for Windows was simplified.

As usual, the new TREEFINDER version can be downloaded free of charge from
www.treefinder.de . There are packages for Windows, Linux and MacOS X.

I wish everybody a Happy New Year 2004!

Gangolf Jobb




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