Questions Regarding ASTRAL Species Tree Inference

[Liuyj-l]

Dear Professor,

I hope this email finds you well. I am currently using your software, ASTRAL, to infer a species tree from window-based gene trees, and I find it to be extremely fast and useful. I do, however, have a few questions that I would like to consult with you:

I am working with 19 species. After alignment, I removed repetitive regions and exons, and then divided the genome into 20 kb windows to build trees with IQ-TREE, without using bootstrapping. However, the assembly quality of some species is low: one species has a BUSCO (S+D) score of only 64%, and two species have BUSCO scores of 89%. Could such assembly quality affect ASTRAL’s inference and potentially compromise the reliability of the results?

In addition, my phylogeny may involve gene flow or incomplete lineage sorting (ILS). Under these circumstances, how would this impact ASTRAL’s inference?

Finally, what would be the best approach to evaluate the reliability or support of ASTRAL’s results in my dataset?

Thank you very much for your time and guidance. I look forward to your reply.