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Pas-Kapli / mptp

mPTP - a tool for single-locus species delimitation
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node supports for speciation in the output tree suggest different result than the number of putative species determined #85

Open pragyr opened 4 years ago

pragyr commented 4 years ago

Hi,

I tried using the multi-rate method on my tree using mcmc. After the analysis, the I found that multiple nodes in the output tree have support values for speciation >0.9, yet those nodes haven't been inferred as speciation events. In my opinion there should be three species in my dataset, as per the support values at the nodes. However the software infers the whole dataset as one species. also the likelihood scores are not converging and the likelihood for the final result isn't significantly different from the null model.

When i tried extracting all the support values from the nodes and tried calculating the Average Support Value (0.98) with the consideration of 3 species, the ASV was substantially higher than the one which comes with the output (0.03).

I am quite confused as to how to proceed.

Pragyadeep Roy

stamatak commented 4 years ago

please post this type of questions on the mptp google group.

thank you

On 17.07.20 13:42, pragyr wrote:

Hi,

I tried using the multi-rate method on my tree using mcmc. After the analysis, the I found that multiple nodes in the output tree have support values for speciation >0.9, yet those nodes haven't been inferred as speciation events. In my opinion there should be three species in my dataset, as per the support values at the nodes. However the software infers the whole dataset as one species. also the likelihood scores are not converging and the likelihood for the final result isn't significantly different from the null model.

When i tried extracting all the support values from the nodes and tried calculating the Average Support Value (0.98) with the consideration of 3 species, the ASV was substantially higher than the one which comes with the output (0.03).

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-- Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.exelixis-lab.org

pragyr commented 4 years ago

Hi, Can you please share the link to the group? I can't find it.

Thanks