For big alignment PHYLIP use big volume of memory, and operating system kill UGENE process.
Steps to reproduce:
1. Open attached file
2. Build phylogenetic tree by PHYLIP with enabled bootstraping.
3. Wait some time, then UGENE will killed.
I think we need run PHYLIP as external tool or through workflow designer.
Crash report: http://ugene.net/ugenecrashes/?id=8830