Software to align sequences - (Nov/23/2012 )

Hello!
I've searched the web up and down, but I wasn't able to find anything... I'm looking for a software product (freeware) which allows alignment of DNA sequences.
I'm doing capillary sequencing of plasmids / PCR samples and want to compare them to a reference sequence. Unfortunately the sequencing computer is not in the same building and it is a Mac (with SeqMan sequencing software on it). I got the sequence files (.seq, containing the native base sequence like TTAGCAG...) and in order to evaluate the sequencing I want to use some freeware on my computer in the office here. Does anyone know good and free software that allows alignment of several sequences, puts them in the correct order and might have a highlighting option for differences in the compared sequences?
Appreciate your help!

Dear 2xzwei,

I am not sure what your exact application is, but if you are looking for a free ware that allows you to upload a reference seq and check for SNPs/ mutations etc. then I would suggest Mutation Surveyor . There is a demo version that you can use for as long as you want.

Its good at picking mutations and can even download the template sequence (provided its human in origin, I guess)

Hope this helps