VNTR data

[Maryam]

Hi,

I am working on a dataset consists of around 2000 microsatellite data with 12 markers. Can I use raxml tool for inferring a phylogenetic tree on my dataset?

Thanks

[Alexandros Stamatakis]

if you can generate a multiple alignment of DNA sequences (or markers) I
guess you can, if this is for very closely related sequences though you
might want to use an ascertainment bias correction, I'd need a bit more
info about the data though to be able to give a more informed answer,

alexis

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Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[Maryam]

Hi,

Thanks for your response.

The data is Genetic data from a TB outbreak in Shanghai, from culture-positive patients.   All TB isolates are assumed to be from the Beijing strain. Around 2000 MIRU-VNTR types (12 markers, including 4 hypervariable ones for the Beijing strain). Please let me know if you need more details.

Thanks,

Maryam

[Alexandros Stamatakis]

that should work in principle with RAxML,

alexis

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>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> Adjunct Professor, Dept. of Ecology and Evolutionary Biology,
> University
> of Arizona at Tucson
>

> www.exelixis-lab.org <http://www.exelixis-lab.org>