How I can do phylogenetic tree using ugene?
First of all, on the web http://ugene.unipro.ru/plugins.html I can't see phylip plugin to downolad, second- when I go to Settings-->Plugins, plugin Phylip is on, so maybe it is already instaled? But I can't find it!

The problem is that I don't have this icon. I have ugene 1.9.1., from http://ugene.unipro.ru/download.html.

One way to start the alignment is exporting a complete sequence as alignment (export_alignment.png) or features from one or several sequences (same feature from two different sequences in Features_alignment.png). Then you can add more sequences, delete, align, etc (check the options with the right button).

After selecting the region (or nothing so it will use the whole sequence), press the icon for "Query Remote Database" (1), then instead of blastn (2), choose ccd (conserved domain database). The advantage of doing that from ugene, is that it will be automatically annotated.
If you are searching for a special pattern, you can do a manual search using Find pattern (3) or the same but using Smith-Waterman algorithm (4). You can also search for transcription factors binding sites (5).
You can also automate this tasks and preform the same over several sequences at the same time using this tools inside the Workflow designer (no number..., go to tools).