[Taxacom] GENERALIZED-TREEFINDER

[Gangolf Jobb]

One more unpaid TREEFINDER version is online at:

www.treefinder.de

TREEFINDER is a software to compute phylogenetic trees from molecular 
sequences.

New features are:

- generalized partition model, which
- includes both proportional and separate model
- resampling of calibration times
- improved TL manual

The generalized partition model covers the assumptions of both 
proportional and separate edge lengths among the data partitions, and 
still a few possibilities more. Partitions can be now organized in 
partition groups assuming a separate set of edge lengths for each 
partition group, but assuming proportional edge lengths within a 
partition group. In a multi-gene framework, for example, one can have a 
separate set of edge lengths for every gene, and also have separate 
partition rates for the codon positions.

Of course, the hypothesis testing and everything has been updated to 
work with the generalized partition model. The groupwise edge lengths 
can be extracted from the reports and saved to a file.

There is a new way of dealing with calibration time intervals: instead 
of optimizing the times within the specified intervals, one can now 
resample them from the intervals in a bootstrap procedure to compute 
confidence limits of divergence times, even with one sample of edge 
lengths of the input tree.

Finally, I added a few more words to the TL manual.

Please note that I am still not being paid for my work and that I had no 
income for years. Seems that nobody here finds
TREEFINDER worth offering me a compensation, a wage, a position, a 
perspective. Seems that I must now change my strategy.

Gangolf Jobb