You don't say which kind of DNA sequence analysis you want to performe... But I understand that you have at least "sequences".
Alignment of multiple sequences:
- Free software Clustal http://www.clustal.org/; MEGA (free for education) using emulsion software.
- Commercial software: genious, CLC Main Workbench (very good but very expencive), Sequencher; DNADynamo http://www.bluetractorsoftware.co.uk/DynamoDemo.htm (free for 45 days) and many others more.
I searched all carolina's list on http://alternativeto.net/software/dnadynamo/ it seems here that Benchling are more popular than DNADynamo. So i suggest Benchling
I suggest you check this tagged software lists:
http://alternativeto.net/tag/dna-sequences/
http://alternativeto.net/tag/dna-editor/
http://alternativeto.net/tag/dna-analysis/
and also type DNA at search and look at top suggestions names of the dropdown list of the mentioned site.