[Taxacom] Software SITEWISE-TREEFINDER

Gangolf Jobb gangolf at treefinder.de
Thu Jun 12 16:47:38 CDT 2008


Another unpaid TREEFINDER version is online at:

www.treefinder.de

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

New features are:

- user-definable substitution model: MAP
- computation of sitewise rates
- automatic generation of data partitions

MAP is a class of general time-reversible substitution models mapping 
characters to states as defined by the user. Multiple characters may 
represent one state. MAP definitions, such as e.g. 
MAP["AGPST","C","DENQ","FWY","HKR","ILMV"], can be stored in variables 
and then be used as building blocks of more complex models. All 
parameters can be estimated. The MAP can be fed into any function that 
takes substitution models, including tree reconstruction, hypothesis 
testing, model selection, sequence simulation.

The computation of sitewise rates replaces the old rate profile tool.

Based on the sitewise rates one can now divide a sequence alignment into 
partitions of slower and faster evolution.

Please note that I am still not being paid for my work and that I had no 
income for years. I wonder if somebody finds TREEFINDER worth offering 
me a compensation, a wage, a position, a perspective. I wonder if I 
should continue or stop the Treefinder project, this programming work is 
not really fun if one is excluded from life. Maybe I'll stop this 
project and better learn how to drive a truck, there's a lot of garbage 
to carry across Europe.

Gangolf Jobb






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