If you have a fasta file of sequences, you can map them to a reference
genome to obtain a SAM file (which you could then compress into BAM).
See the tool section "NGS Toolbox".
BLAST is an alignment tool and additional parsing/analysis tools would
be needed in order to identify SNPs. If you do your analysis this way,
and SNPs are called outside of Galaxy using your own methods, the
output could be converted into a format such as BED. Then Galaxy could
be used to perform analysis vs public SNP databases.
To locate the SNP tools available Galaxy, in the left pane of the UI,
choose "Options -> Show Search Tool" and enter the keyword "SNP".
Please let us know if you would like help with any of the tools,