We are applying your tool across nine species to test if there is stronger evidence of ancestral WGD in one species vs. the others. The tool is working very well for us (with the exception of "pairwise" mode generating empty plots after ksd, maybe because of a missing "Node" column in the output file?).
I wonder what signature I should preferably look at to distinguish between the evidence of WGD between species. What overall statistic captures the fit best such that it can be compared across species?
For example, is it reasonable to contrast a 1-component vs. 2-component model to check the overall fit and test what proportion of gene families become associated with the second component in each species?
Dear developers,
We are applying your tool across nine species to test if there is stronger evidence of ancestral WGD in one species vs. the others. The tool is working very well for us (with the exception of "pairwise" mode generating empty plots after ksd, maybe because of a missing "Node" column in the output file?).
I wonder what signature I should preferably look at to distinguish between the evidence of WGD between species. What overall statistic captures the fit best such that it can be compared across species?
For example, is it reasonable to contrast a 1-component vs. 2-component model to check the overall fit and test what proportion of gene families become associated with the second component in each species?
Any pointers are valuable here.
Thanks for a great tool!
Cheers!