pxltr should preserve annotations if present

[josephwb]

pxltr works well, but if the input is an annotated Nexus tree, the newick output does not include the annotations.

[josephwb]

Rethinking this one. Are Nexus annotations newick-compliant? Don't think so. Forget how this got brought up.

(If someone remembers, let me know! )

[blackrim]

@josephwb do you have an example with this? I can help tackle this but not exactly sure I understand it.

[josephwb]

This so old I forget! Also, must be pxrlt?

But I think the situation was this: you have, say, a BEAST tree with ugly labels. You use pxrlt to clean them up, but because a newick comes out all of your fancy Nexus node annotations (probabilities, rates, whatever) are lost, so when you open your tree in FigTree you cannot make it pretty.

But I guess this would be a an issue for most programs. Maybe a general solution is to have have Nexus as a possible output option? I am currently doing that for pxcltr.

I can look at this.

[coyotree]

Just curious if there are any updates on this?

[blackrim]

I would also like this functionality, but don't know if @josephwb had already assigned it to himself. @josephwb are you doing this?

[josephwb]

I am not currently working on this. Basically, we need a general Nexus tree writer that preserves the annotations. This should be made as an available output option for pxrlt and pxrmt and pxrr (maybe others?).

[sbrobeson]

I would be interested in this if it does ever come up again. I have an annotated Nexus treefile from pxcontrates in which I would like to preserve the ancestral state reconstruction values, but of course running it through pxrlt got rid of them. I know for now that the thing to do is use pxrlt on the starting tree that I run through pxcontrates but I could foresee more general needs for this, like with BEAST output as stated above.

[josephwb]

@sbrobeson Thanks for pinging this issue. I agree it would be of use. I am working on several other issues, so if anyone else wants to run with this, that would be great. Otherwise, I can come around to this at some point.