[Taxacom] MIXED-PROTEIN-TREEFINDER

[Gangolf Jobb]

A new unpaid TREEFINDER version is online at:

www.treefinder.de

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

New features are:

- mixed protein model: MIX
- Dayhoff groups protein model: DG
- improved model proposer

A mixed protein model MIX[B1,B2,...] is a linear combination of 
empirical base models B1,B2,... with weights that are optimized along 
with the tree. More precisely, their parameter vectors are combined. The 
MIX does interpolate between the base models, and also extrapolate when 
weights are negative. The MIX does often fit data much better than any 
of its base models alone. The user decides which and how many models to 
mix, the complexity depends on the number of models included. Given 
enough independent base models, the MIX allows to model any kind of 
linear dependency between the amino acid replacement parameters, and 
with 190 or 210 independent base models the MIX becomes equivalent to 
the 20-state GTR.

The MIX does also work with 20-state RNA models.

The model proposer proposes MIX'es if they are appropriate.

The model proposer does now display the scores and parameters of all 
models tested. User-defined candidate sets are possible.

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.

Gangolf Jobb