Protein MSA tools - Which is best for conserved domains and divergent protein extensions?

Question

[arosa]

My question: Which Multiple Sequence Alignment method to use to align proteins with evolutionarily conserved domains and divergent (sometimes, structurally or with no structural data available) protein extensions?

Any tips/best practices on this topic? Is PRANK better than PROMALS3D better than MAFFT in this? Thanks!!

[Ram]

Titles should be concise and to the point. Descriptions belong in the actual text. I've made some changes for you :-)