SNP only analysis in RAxML

[heidi]

Is it appropriate to use ONLY SNPs  to construct an ML tree?  I will have a large data set produced by GBS (genotyping by sequencing) and thus it will  contain SNPs only without any neighboring/invariate sequence. It also will have lots of missing data.  I am evaluating what options I have to reconstruct a phylogeny based on such data.  Is ML (and Bayesian) and option?  I'd also appreciate references that address this topic. Many thanks for your input    Heidi

[Alexandros Stamatakis]

Dear Heidi,

You can use RAxML but the models in there do not implement likelihood
models that accommodate ascertainmant bias yet, i.e., models that
correct for the fact that you only include variable sites (in this case
SNPs) into your datasets and omit the invariable ones.

We are working on this though,

Alexis

--
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

[George Pacheco]

My dear Alexis,

I also got a SNPs data set generated by GBS and as Heidi I am very willing to reconstruct a phylogeny using it. Thus, I want to kindly ask you - would you have any prevision when a model that can deal with such data will be implemented in RaxML?

Thanks in advance for your attention, George Pacheco.

[Alexandros Stamatakis]

see the new manual:

http://sco.h-its.org/exelixis/resource/download/NewManual.pdf

pages 24 and 25 :-)

Alexis

[George Pacheco]

Sincere apologies Alexis, I had read precisely that part and I am not sure why I did not see it - so clear. Running the program now !

Thanks and I wish you a Marry Christmas.

George Pacheco

MSc Student in Biology and Student Assistant

________________________________________________

COPENHAGEN UNIVERSITY - FACULTY OF SCIENCE

Department of Biology

Centre for GeoGenetics - Natural History Museum of Denmark

EvoGenomics Group

Øster Voldgade 5-7, 1350 Copenhagen K

Contact: (45) 2483-2451

2013/12/21 Alexandros Stamatakis <alexandros...@gmail.com>

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