Questions related to Relax analysis

[T-164321]

Dear Author,
First of all, thank you for providing us with such an excellent software tool. During its use, I have encountered several questions and would appreciate your guidance:

Are there any specific requirements for the tree file when performing Relax analysis? I currently have three types of trees: one with divergence times, one with branch lengths (phylogenetic tree), and one with only topological structure. (This is because I obtained different results using the tree with divergence times and the tree with branch lengths.)
I have selected 14 species as test branches, but I am not sure if the {FG} display is correct. (The tree file provided includes annotations.)
The link contains the code I used, and I am not certain whether it is correct.
I have stored all relevant information in the link provided. Could you please take a look and help me with these questions? I look forward to your reply.

tissue.txt

[stevenweaver]

Dear @T-164321,

1. Do not use the divergence time tree because RELAX requires a molecular substitution model, and time-scaled trees do not reflect mutation rates. The tree must be ultrametric (i.e., branch lengths must reflect molecular evolution, not absolute time).

2. After running the RELAX command, open the JSON output (ENSP00000000233.fa.json) and look at the "tested" section. If your 14 test branches are not listed as "Test", the {FG} labels may not have been interpreted correctly.

Potential issues in your command:

1. Ensure the tree is in Newick format and contains branch lengths (substitutions per site).
2. Ensure that species names in the tree exactly match sequence headers in the alignment (.fa) file.

Best,
Steven

[T-164321]

Dear @stevenweaver
Thank you for your reply. I have understood. Thank you.

Wish you all the best.