Using OrthoFinder, input the fa protein file downloaded from NCBI and obtain species tree. Is this species tree very correct?

[helloworldABCD1234]

Using OrthoFinder, input the fa protein file downloaded from NCBI, and use the "OrthoFinder - f./" command to obtain the species tree in the species folder. Is this species tree very correct? Why do some branches have low confidence ratings of around 25-35, while others have a rating of 100.

[lauriebelch]

Hi,

It's hard to say really. The latest version uses ASTRAL-PRO to infer the species tree, which is an accurate method.

Websites such as https://timetree.org/ or papers in the literature can often be good ways of getting an accurate species tree