Site Models for FBD analysis

[Nitish Narula]

Hi,

I was wondering how to partition a DNA alignment and assign corresponding models in FDPPDIV. We have a dataset containing 748 taxa and ~10k sites which includes 24 partitions. The starting tree was generated with mrbayes using partitions determined with 'partitionfinder'. Is there any way to use the same information about partition models in FDPPDIV? I guess a more basic question would be: is that even relevant for FBD dating divergence analysis? (I would think it is).

Thank you,

Nitish Narula

[Tracy Heath]

Hi Nitish,

Currently, DPPDiv does not support partitioned models. This is something that is in development, but not available yet. It may be better for you to try this in BEAST2 if you are interested in using the FBD model. Sasha Gavryushkina has released a package that uses the FBD model and can be used to calibrate the tree (see their preprint and re-analysis of the bear dataset http://arxiv.org/abs/1406.4573). I believe that she and Alexei Drummond are currently working on a new tutorial that explains how to use their sampled-ancestors package to perform these analyses. Additionally, we are implementing the FBD model in RevBayes, which will be released this year.

Cheers,

Tracy

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[Nitish Narula]

Thanks for the reply, Tracy. I did get in touch with Sasha and Alexei about their plugin for BEAST2. Hopefully I can get that going soon.

Best,

Nitish