Hello,
I use Geneious and installed the RaxML plug-in to run maximum likelihood phylogenetic analyses.
When running a neighbor-joining tree build, I get what I would expect to be the substitution rates. (For example, 0.04 for clade A.) One note, I am running rapid bootstrapping when building the ML tree. Not sure if that is the issue.
Any suggestions?
Thanks,
Peter
Another issue I'm having is that my outgroup clades closer to on clade in particular within my tree than any other of the others. Granted, the tree shows the outgroup to be significantly more distant but it branches off a specific clade. Is this acceptable?
The distances on your tree are not substitution rates, they are phylogenetically corrected distances. If you know something about the dates when your organisms shared common ancestors, the distance:date relationship can be used to infer overall rates.
I really can't guess what you mean by "branches off a specific clade" without seeing a tree and knowing something about the type of organisms you are studying.
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