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naturalis / supersmart

Self-Updating Platform for the Estimation of Rates of Speciation, Migration And Relationships of Taxa
MIT License
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Running without backbone tree #91

Closed fernandafreitas closed 8 years ago

fernandafreitas commented 8 years ago

HI, I'm trying to use supersmart for a while, but now I realized that since the biggest genus in the group i'm studying is polyphyletic, I shouldn't produce the backbone tree. But I don't know which command I have to use to do that. I tried "smrt bbmerge -e -1" but it is not working.

Does anyone have a better idea?

Thanks

rvosa commented 8 years ago

Hi Fernanda,

the fact that the genus is polyphyletic doesn't necessarily mean you shouldn't build a backbone: the key is to convince the pipeline not to assume that this genus is monophyletic.

The backbone needs to be decomposed such that you end up with at least a decomposed clade that includes both your polyphyletic genus as well as the other genera with which it is entangled, in addition to the other decomposed clades for the other genera (which presumably are monophyletic).

What then is supposed to happen is that this polyphyletic genus is resolved further, in combination with the other genera with which it is entangled, and that this whole subtree is then grafted onto the backbone.

You are right to think that a sensible way to do this is to issue "smrt bbmerge -e -1" so what we need to do is figure out what you mean by "not working", and fix that. So what is happening when you issue "smrt bbmerge -e -1"? What gets written to the terminal?

Rutger

On Thu, Feb 4, 2016 at 11:15 AM, fernandafreitas notifications@github.com wrote:

HI, I'm trying to use supersmart for a while, but now I realized that since the biggest genus in the group i'm studying is polyphyletic, I shouldn't produce the backbone tree But I don't know which command I have to use to do that I tried "smrt bbmerge -e -1" but it is not working

Does anyone have a better idea?

Thanks

— Reply to this email directly or view it on GitHub https://github.com/naturalis/supersmart/issues/91.

hettling commented 8 years ago

This was an issue caused by an old virtual machine, where the '-e' option for bbinfer was not yet available.