[Molecular-evolution] Obtaining rate categories file for PROTDIST
in large datasets
tmargus at ebc.ee
Fri Feb 17 08:17:02 EST 2006
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
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
Department of Bioinformatics
Institute of Cell and Molecular Biology
University of Tartu
Riia str. 23, Tartu 51010, Estonia
email: tonu.margus at ebc.ee
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