This is an online calculator, it makes it faster:
You have one gene but several alleles for this gene in 10 species.
“Shall I use one allele per species (I don't have frequencies) or all alleles per species” ?
If you take one allele per species, how will you choose which one to select?
I would try to take all alleles per every species at first,
align them with the calculator above or somehow else – it will show you how different they are
and find allele consensus according to the post below.
Test of selection across whole genomes
Here Nicolas suggested to choose allele consensus.
In this post PAML Batch File? a pairwise topic is discussed. See @Brice advice in the end.
My impression is that there is no strict rule how to accomplish the task.
I would find a close target organism and study how people dealt with it before.