No option for returning the dictionary using the alignment order, only the input order.

[beowulfey]

The Clustal Omega binary has a command line option for "output-order", which allows for returning the alignment using the order provided by the alignment tree. Unfortunately, the API doesn't have an option for this, which is why I suspect it's not an option in this wrapper.

I managed to track down how Clustal Omega translates that command line option into output and recreate it in the wrapper. So long as the space for tree_order is allocated in the prMSeq, the tree-order is calculated automatically. So we can access it from the wrapper!

I'm going to create a pull request that has the additional "output_order" keyword added as an option. I think it is working properly.