Mike Lee

Hi there, Jianshu :) Thanks for the note, I didn't know about veryfasttree yet. Seems invaluable for large trees! I think you're right that the conda install only supports avx2,...

Note for myself, it looks like as of a few weeks ago this might be more flexible to OS based on the recipe update [here](https://github.com/bioconda/bioconda-recipes/pull/50759/files) 👍 I need to investigate

since the conda recipe has been improved to deal with mac/darwin too under-the-hood (and i finally got around to testing it), this is included as a treeing option as of...

Hey there, Molly :) Thanks for writing in! So the main thing you hit on (regarding how GToTree deals with multi-hits) has changed since i put the original paper out,...

Heya, @ezherman :) Do you still get no hits if you run it in "best-hit mode" by adding the -B flag? Or just looking at the count summary table produced...

Ah, i see the deal now, @ezherman. GToTree relies on "gathering thresholds" (GA) to be included in the HMM files like this:  And Molly was probably using a different...

Heya, @raufs! Yea that's a good idea – looking into the eukaryote set and just adding in their provided score cutoffs as GA values should let me make a cat'd...

## Review checklist for @AstrobioMike ### Conflict of interest - [x] As the reviewer I confirm that I have read the [JOSE conflict of interest policy](https://github.com/openjournals/joss/blob/jose/COI.md) and that there are...

Sorry for my lack of timeliness, @sambit-giri and @arm61. @sambit-giri, you've done excellent work on this! I don't have any required changes from my point of view. Just some small...