bali-phy-users

Hi Ben, Thank you for getting back to me and apologies for the late response. The use case I was

Hi Ben, I am using bp-analyze to check if my runs have converged by running it as so: bp-analyze run-

That's actually fine. I'll probably hide that message in the next release. It just means that

Hi Cedric, I checked that this command works on the binaries of 4.0-beta2 released on github. Did you

Hi Ben, We can't use Docker at present, due to security concerns on our HPC machine. However, I

Hi Ben, Thanks for the prompt reply! Good luck on tracking down the increase in memory usage :) Wayne

Hi, I was asked what "indel groups" means in the "alignment-info" program. Here

PR created. Hopefully, I didn't mess up anything. I used a Mac (case-insensitive file system),

Hi, Points #1 and #2 make sense and clarify the behavior of BAli-Phy. Regarding your question in #3

Thank you, I fundamentally misunderstood m8/m8a models. This makes perfect sense. Karolis On Monday,

Thanks, Benjamin, Personally, just knowing that the branches should be rescaled by a partition-

Hi 鑫鑫, Did you run bp-analyze? If so, did you look at the generated file "index.html" using

Hi, Ben, and thanks for the tips, particularly the suggestion to condition on the subtrees matching.

Thanks for the linuxbrew tip. As workarounds go, for anyone else that finds this: the seg fault was

Hi Douglas, Interesting ... that's unfortunately that SVG is unavailable for some platforms! I

Hi Tyler, Thank you for the files. It looks like creating the ancestral sequence alignment was both (

Great! Its good to have these kinds of problems/solutions available on the mailing list archives. -

Hi Maya, Oh, I see. I think I should refer you to the "Probabilistic Model" section of the

That looks very helpful! I am new to using Bali-Phy, and will need to talk with my advisor about the

Hi everyone, In case anyone has had trouble compiling version 3.5.0 from source, I've released

Thanks for the report! I'm going to follow this up on the issue that you filed. -BenRI On 6/24/20

Hi Ben, BTW, would you mind sending questions to the google group, so that other people can benefit

I guess I should point out that if you use a site model, such as m8a, then the tree and the alignment

Dear BenRI, Thank you so much for your kind reply and very detailed explanation. Sorry for replying

Thank you, Ben! this has all worked perfectly and I can now visualise the results too in FigTree and

Just re-downloaded it onto the cluster - it works now! Thank you!! On Monday, April 20, 2020 at 2:29:

Hi Michael, Thanks for the bug report! 1. Just to make sure I'm understanding you correctly, are

Hi Cynthia, I think the problem is that the root is placed on a leaf node. I will try and fix this

Hello, Are there any plans to allow for missing data in an analysis? I saw the previous answer about

Hi, Thanks - I should have looked! The greedy tree is fine for me, so I'm not waiting on a fix!