[BiO BB] Phylogeny trees on many sequences?

[Stefan Rensing]

Burke,

you might want to think about using MAFFT (Katoh,K., Misawa,K., Kuma,K.,
and Miyata,T. (2002) MAFFT: a novel method for rapid multiple sequence
alignment based on fast Fourier transform. Nucleic Acid Res.,
30:3059-3066,
http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/), which is
well suited for large numbers of sequences.

Concerning trees, you could use e.g. a combination of PHYLIP and
TREE-PUZZLE, combining ML branch lengths and the speed of NJ trees, i.e.
bootstrapping -> ML distance matrix calculation -> NJ trees -> ML
consensus tree.

Cheers, Stefan

Burke Squires wrote:

> Hello,
> 
> I am working on assembling phylogenic trees on multiple sets of large 
> numbers of sequences, in some cases more then 3000 sequences. What is 
> the best way to align these sequences and assemble a tree? I am 
> interested in trees which calculate the lengths of the branches.
> 
> I have dome some multiple sequence alignment using muscle which works 
> in a reasonable amount of time. However, what options are available  for
> creating trees from muscle output?
> 
> Sincerely,
> 
> Burke
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-- 
Dr. Stefan Rensing, Group Leader Computational Biology
Plant Biotechnology, Faculty of Biology, University of Freiburg
Schaenzlestr. 1, D-79104 Freiburg, Fon: +49 761 203-6974, Fax: -6945
http://www.plant-biotech.net/  http://www.cosmoss.org/
stefan.rensing at biologie.uni-freiburg.de

"An old man dies. A young girl lives. A fair trade. I love you, Nancy."