[Molecular-evolution] Obtaining rate categories file for PROTDIST in large datasets

Tõnu Margus tmargus at ebc.ee
Fri Feb 17 08:17:02 EST 2006


Hi,

 

I would like to use more realistic model for calculating protein evolution
tree. It is known that all positions in proteins don not evolve with the
same rate. So, more realistic model should contain rate categories. When you
had many sequences then quiet often distance based methods seems to remain
reliable choice.

 

Can someone give an advice how to get rate categories for PROTDIST (PHYLIP),
when you dataset is large?  The TREE-PUZZLE can calculate rate categories
together with computing quartet puzzling tree, but when you dataset exceed
puzzling limit - 257 sequences, then it can not compute puzzling trees as
well as do not give in its output rate categories positions on alignment. 

 

 

Are there some good solutions for this problem?

 

 

 

Thanks in advanve

 

Tonu Margus

 

 

 

 

 

========================================

Tonu Margus

Department of Bioinformatics

Institute of Cell and Molecular Biology

University of Tartu

Riia str. 23, Tartu 51010, Estonia

tel: +372-7376037

email: tonu.margus at ebc.ee

web: http://bioinfo.ebc.ee/ 

 

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