When the same site in the target branchs is detected in a branch other than the ancestral branch for the target branch, is this still a convergent site of the target branch?

[aaannaw]

Hello I am running the pipeline to detect convergent sites for target branches, however I got the weird result, as showed in the following picture. The E and T represented corresponding site. The red "T" represented the site of target branches for detecting convergence.
I've read your article and documentation, and I see that you consider the target branch to be at a consistent site, and different from the corresponding ancestral branch. This locus meets this criterion, however, the convergent site for target branches is also with the same target branch in the outgroups 3_Hcr, do you consider this case to be a convergent site as well?

[ztzou]

Hello. If the external branches leading to 5_Hgl and 13_Fdm are your target branches, and the ancestral states are well inferred as shown in the figure, then this site is a convergent site that you are interested in. Our method does not require the derived, convergent state to be unique to focal taxa and cannot appear in the background taxa. However, scientifically, you could add this constraint to your analysis pipeline, which will then render this site not convergent (not a "conserved convergent site"). This is up to your design and preference for stringency. Thanks for using our method.

[aaannaw]

Hi, Thanks for your response. I have added the constraint to assure that those shared site in target branches can not appear in the leaf species. Perhaps, do you have any shared scripts to filter out those shared site in both target branches and other internal astral branches? Best wishes Na Wan