you can use CLC Genomic Workbench 6.5 software, it has a lot of applications including alignment and sequence assembly. you can download a trial copy, and it will be available for 1 month for free
I use BioEdit for alignment, and for all sequence manipulations. It's very good, with a number of options, user-friendly and free! http://www.mbio.ncsu.edu/bioedit/bioedit.html