which parameters should I use with the "lot of missing data"?

[liamxg]

Dear @stephaneguindon,

Could I know which parameters should I use with the "lot of missing data"?

Thanks.

[stephaneguindon]

I'm not sure what you mean here. What "parameters" are you referring to?

[liamxg]

Hi @stephaneguindon,

When I removed the recombinant regions, some sequences have very long missing regions, how to set this kind of data for PhyML?

Best,
Liam