What would be a good starting point for a newby? Is there a good and up to date manual? A collection of howto? What does Ugene include nowadays?

First of all, thank you for using UGENE and writing us!

I think a good starting point is watching our podcast over there (http://ugene.unipro.ru/documentation.html). There are a lot of videos, just pick those that are close to your task.

There is an up-to-date manual here(http://ugene.unipro.ru/documentation.html)

1. You can drag a sequence in msa using mouse to reorder the sequences. And extract a subsequence/subalignment using a popup menu item("Export").
2. Select a sequence or subalignment and hit the space button (delete button) to insert (delete) gaps.

If you have any other questions about UGENE feel free to ask!