A. Murat Eren (Meren)

@metehaansever, https://github.com/merenlab/anvio/pull/2364/commits/3084b8f41d2eb69b3c6d7911d1f21a921173b9ed should fix the bug above. Please test :)

We have a similar solution for anvi'o workflows -- see an example here for third-party tools used: https://anvio.org/help/main/workflows/ecophylo/ Perhaps we can use this mechanism also in programs :)

Hi @AshSudarshan. Thanks for bringing this up. To be honest there is no absolute threshold to cite here, and 0.3 is just another made up cutoff, just like every other...

Well, I started doing some checks. Here is a stupidly over-engineered BASH script (`test.sh`) to switch back and forth in anvi'o branches and run a test Python file (`test.py`) that...

Thank you very much, @ivagljiva! Good solution. As you suggested, I'll merge it, and let people know in Discord so they're aware that there may be some hiccups and we...

Thanks for this, @dspeth. I think it is time we think about a flexible way to export defline information for all FASTA files. In an ideal world, the user should...

This branch is finally merged. Thank you again for your input and guidance, @dspeth.

Hey @dspeth, Very sorry for the late reply. 2 weeks ago I was at a conference, and last week I was on a break, so this kept being pushed. I...

Hey @metehaansever, can you please try to reproduce this? You can use `anvi-self-test --suite mini -o TEST`, and then `anvi-interactive` in the `TEST` directory with `-C` :)

@jwilliams648, what are your collection names (if they are starting with numbers it can cause some problems for the tree parsing library perhaps)?