Extracting placements from specified clades

[mjamy]

Hi Lucas!

Hope you're doing well!

I have a (hopefully quick) question about extracting placements from clades using the subcommand extract.

I'm a bit confused about whether gappa extracts placements from the stem branch of the clade as well or not. To illustrate, I'm attaching an image comparing my output (using the flag --color-tree-file) to the figure from your 2017 NEE paper with "Radiozoa" highlighted. If I understand your study correctly, OTUs placed in the stem branches (highlighted in grey) were discarded. I'm wondering how I can replicate the analysis, as it seems placements on the stem Radiozoa branch would be included in my case.

Thanks a lot!

Mahwash

[lczech]

Hi Mahwash,

good point, that indeed was not possible with the command, and differed from the way we did it in the article. Luckily, I had already implemented the functionality, and just not exposed it via the command line interface of gappa, so that was quick to fix.

The new release gappa v0.9.0 now contains an option --exclude-clade-stems to do what you want. I've also renamed the basal_branches output of the command to simply basal, but also added options to rename that and the uncertain clade. And I've moved the command to the edit module, which seemed more fitting - as you were not aware of that command as well, I guess it was not very findable where it was before, and I hope that helps.

Closing the issue for now, but let me know if that works for you, or if you have any more trouble or suggestions :-)

Cheers
Lucas

[mjamy]

Wow thanks Lucas for the very quick fix and thorough response!!

I'll try it and let you know if I run into trouble. I expect it will go smoothly though ;)

Cheers,
Mahwash