Clustal Omega is a slower but more precise algorithm compared to MAFFT. In anticipation of more long-running alignments, we've upgraded our alignment servers and tweaked the alignment UI. Instead of a giant loading message, in-progress alignments show up in the alignments panel and leave you free to do other work while waiting:
This update also exposes some alignment parameters (both for MAFFT and Clustal Omega) for power users to tweak:
As a final bonus, for the python developers out there we've written a small Python wrapper for the C API to libclustalo. Check it out on GitHub: https://github.com/benchling/clustalo-python.