[Taxacom] DISTANCE-TREEFINDER

[John Grehan]

Ok, so I am ignorant of many things and admit it. 

So from the list of new features referred to below am I correct to
understand that distance measures, and techniques of least squares
fitting are phenetic rather than cladistic measures of similarity?

The DNA and protein models. Are these where one theorizes how the
phylogeny should have proceeded and then see how well the data fits?

John Grehan


> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of Gangolf Jobb
> Sent: Monday, March 31, 2008 5:49 AM
> To: taxacom at mailman.nhm.ku.edu
> Subject: [Taxacom] DISTANCE-TREEFINDER
> 
> 
> 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:
> 
> - computation of pairwise ML distances
> - construction of distance trees: NJ, BIONJ
> - least squares fitting of edge lengths
> - more DNA models: J1, J2, J3 (= TIM), TVM
> - more protein models: betHIV and witHIV
> - improved model proposer
> - more efficient TL
> 
> Distance trees can be built under topological constraints.
> 
> The models J1...J3 represent the 3 possibilities of joining two and
two
> transversion parameters of the GTR. They have 3 free rate parameters
> and, together with the TVM, they fill the gap in complexity between
the
> TN and the GTR. The model proposer proposes the new models if they are
> appropriate.
> 
> The TL interpreter is now three times faster and uses half the memory
of
> the previous implementation.
> 
> 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
> 
> 
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