Thanks to augur import it is now possible to import BEAST MCC trees. You must certainly know that BEAST is a very powerful tool and therefore an input of interest for nextstrain.
However, there is currently little documentation on this subject.
So, do you know whether it is better to import a discrete BEAST tree in order to trace phylogeography?
Thanks in advance!
I’m not quite sure what the choices are: discrete BEAST tree, or? Maybe @james can help?
Hey @kelianP – happy to help any debug specific errors you have with
augur import beast. The question of discrete vs continuous phylogeographic models is dependent on your data, and perhaps the BEAST forums / tutorials would be a better place for this.
Hey @james , @corneliusroemer thanks for your reply - In fact, I would like to build a continuous phylogeographic model for my data. However, even though my metadata seems to be correct and thus the phylogenetic tree too, I am not getting satisfactory results.
I was asking the previous question because most of the pathogens already submitted seem to be represented by discrete models. I guess these models were chosen by the maintainers, and not because this could be a limitation of Nextstrain?
Nextstrain’s bioinformatics toolkit (“augur”) cannot reconstruct continuous phylogeography, but BEAST can!
To bring an update. I’ve started from a continuous phylogeography reconstructed by BEAST (using augur import beast) and after discretizing it, I can finally have a correct visualisation under auspice.
Thanks for your answers !