We think that the problem might be due to the number of sequences (200) or to fact that we only have a single calibration node, (11-22 m.y. at the base node of the phylogeny).
We have tried to use different formats for the starting tree, but none of the possible options has been useful!!!!!
When BEAST is not given any tree, it runs but we get something like this (negative branch lengths and incorrect taxonomic groups).
We just tried all in the online foros
Here is the message:
Error 110 parsing the xml input file validate and initialize error: Sample from prior flag is set, but distribution with id 'likelihood' is not an input to posterior.
Error detected about here:
Many thanks!
S
Hi,
I, Pedro P write to you all for I have been trying for quite some time to get my trees (originally derived from MrBayes 3.2.5) fixed in the xmls generated with Beauti in order to get the estimation of the evolutionary rates of the distinct clades and taxa, without the quite troublesome assumption of Molecular Clock for my analyses and without having to deal with the trees generated by Beast given the constitutive widespread failures generated within, including in branch lengths and obviously in the evolutionary rates (my endgame), using of course GTR and Random local clock or flexible log-normal clock. However, I'm still far from an expert in the xml editing procedure and not just one, but both current procedures for fixing the tree with xml editing described on Beast2
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