Hi martin

I think there is any software, u have to done ur BLAST in databases anyway

but

try this software

Bioedit

u can done multiple alignment adn clustalW..

http://ugene.net/

Try Unipro Ugene, you can find tutorials on YouTube, for this purpose. It is full NGS analysis open source software.

You can use Standalone BLAST, to run BLAST programm using command line on your computer. It will help you create a database form your data and perform BLAST search.

https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download

you can find the software and the relevant tutorial and documentation.

Yes, standalone BLAST is how I would do it (and have done in the past). You can interface it with python etc.