Lucas Czech

Hi @kawabata-tomoko, thanks, that makes more sense now :-) > Should I set the model to be consistent with the actual tree or should I change the MSA type input...

Hey @atoselan, as far as I am aware, as long as you get a newick tree and its model parameters in some form that EPA-ng understands, that should work. See...

Hm, if I recall correctly, hmmer/hmmalign uses a flag `-m` to keep the length. I'd check their manual :-)

And another bump from me to increase urgency :-)

Hi @lparsons, I have not found a solution yet. But using mamba instead of conda definitely helps to alleviate the problem. In my case, for some GitHub CI jobs, it's...

Ah sorry, yes sure: Ubuntu 20.04.2 LTS Atom 1.57.0 minimap 4.39.14 minimap-git-diff 4.3.6

Hm, it was working fine a few days ago. Not sure what changed since.

Okay, thank you for the info! I guess we'll just wait for atom/minimap to fix this :-) Or is there anything else that we can do here? If not, feel...

Same here. How can I increase the time limit?

There is a very small Bipartition class in ./lib/tree/, which can extract Bipartitions so far. In the future, we should build in your ideas, I agree.