Does Garli online version calculate the bootstrap consensus tree?

[Cynthia Asorey]

Hi everyone!

I´m a new Garli user. I have done a ML analysis in online Garli version. This version gave me two .tre files, one called all.boot.tree and the other bootstrap_consensus.tree. Before that, I read in the Garli manual that this software DON´t calculate the bootstrap consensus tree and that I have to use some another program to calculate it (e.g paup). Is the online version different to command line version? 

Other question is about partition analysis in online version. I wrote the partition in the nexus file and the different models in the web page, but when download the garli.conf from this, It have not the models block ¿Is it normal or Garli can´t read the models that I had written in?

Thanks in advance

Cynthia 

[Adam Bazinet]

Hi Cynthia,

Yes, the GARLI web service at molecularevolution.org does in fact calculate a 50% majority rule consensus tree for you (using Sumtrees); some of this is explained briefly here: http://www.molecularevolution.org/software/phylogenetics/garli/about

Information about the consensus tree construction will also be present in comments in the header of the bootstrap_consensus.tre file.

As for your question about the partitioned analysis, please write to me directly about it (adam.b...@umiacs.umd.edu) and include the job ID and I'll look into it further for you.

best,

Adam