Question Regarding Relax Analysis Results (K = 0)

[aaannaw]

Dear author,
Based on the results of the RELAX analysis, I observed evidence of relaxation (K < 1) or intensification (K > 1) of selection on the test branches compared to the reference branches. However, I noticed that for some genes, K is exactly equal to 0, which might suggest extreme relaxation. I would like to confirm if this interpretation is accurate or if it might indicate a potential issue in the analysis or data.

Thank you for your guidance.

Best regards,
Na Wan

[spond]

Dear @aaannaw,

Generally K=0 is indicative of some sort of convergence or model fit issue. Can you provide an example?

1. The relax command you ran.
2. The input files.
3. The output your observed on the screen.

Best,
Sergei

[aaannaw]

Dear author
Thanks for your response.
My command is /data/01/p1/user157/software/hyphy/bin/hyphy relax --alignment /data/01/p1/user157/Bathyergidae-sociaty/2024812.newcactus/03.proteincoding-selected-analysis/01.getgene/07.deletestopcodon/evm.model.ptg000009l.54.fa --tree /data/01/p1/user157/Bathyergidae-sociaty/2024812.newcactus/03.proteincoding-selected-analysis/01.getgene/13.hyphy/02.relax/00.mark.tree/evm.model.ptg000009l.54.fa.treefile.mark --test FG1 --reference FG2 --output /data/01/p1/user157/Bathyergidae-sociaty/2024812.newcactus/03.proteincoding-selected-analysis/01.getgene/13.hyphy/02.relax/01.socialtest.relax.out/evm.model.ptg000009l.54.json > /data/01/p1/user157/Bathyergidae-sociaty/2024812.newcactus/03.proteincoding-selected-analysis/01.getgene/13.hyphy/02.relax/01.socialtest.relax.out/evm.model.ptg000009l.54.log 2>&1
The input tree is unrooted genetree rather than species tree:
[evm.model.ptg000009l.54.fa.RELAX.json](https://github.com/user-
(Hcr,(((Gca{FG2},((((Fmi{FG1},Fan{FG1}),Fme{FG1}),Fda{FG1}),Cho{FG1})),Bsu{FG2}),Hgl{FG1}),((Pty,Tsw),Cgu));.
The input alignment file evm.model.ptg000009l.54.fa.txt , the output log file evm.model.ptg000009l.54.relax.log and json file evm.model.ptg000009l.54.fa.RELAX.json are attached.
evm.model.ptg000009l.54.fa.RELAX.json
evm.model.ptg000009l.54.fa.txt
evm.model.ptg000009l.54.relax.log
Best wishes,
Na Wan