Pierre Barbera

Hi @RachelDanie ! It's pretty surprising that the first way you tried it (with raxml-ng) didn't work... did you supply that model string on the command line? Can you try...

Unfortunately partitioning is not currently supported in epa-ng. However if you are sure that your query sequences are from just one of those partitions, then I strongly advise that, at...

- you should obtain the model parameters AND the tree with corrected branch lengths from `raxml-ng --evaluate`, which you feed with your tree inferred from the full alignment - use...

You can still do it as I outlined and it won't make a difference, because the taxa that don't have signal where the queries align will essentially be ignored, since...

I think I will revise my last statement to: (I think) you can in theory do the placement on the trimmed alignment, at least from the perspective of EPA, but...

Hi David, thank you for bringing this to my attention. So the bug here seems to be that not all branch lengths get set from 0 to that value. Setting...

Hi David, in your described scenario there would be two identically likely placements at the Human and Gorilla terminal branches, since there is no signal to distinguish between them. Thats...

EPA-ng can parse IQTREE log files yes, but I made that more of a hidden feature since I'm pretty sure (as you say) I don't/maybe can't support all models coming...

Hi @michoug! Thank you the suggestion, I hadn't heard about those models yet. I think this is something that may be added to the underlying phylogenetics software library in the...

Hi @edmundtayzy, what error does it show? Or does it simply abort? If it just aborts its likely that you ran out of memory. Try to run the script with...