Imagine the following situation:
You have a 454 read, which means a relatively long read. You can first perform a mapping (using for instance bwa-mem) to some reference genome and check for a following situation: If you have a region of the genome where you can find two sets of reads, one with a mutation in position x, and the other with the mutation on the position y, then you can be pretty sure you are dealing with 2 strains.
You can also try to perform the de novo assemblies (with for instance Vicuna) and see if you get different contigs for the same positions (as regards to some reference genome).
I would look for regions which are covered with more than one set of corresponding reads.
Also, I have previously found software that tackles this problem, but am somehow unable to do so now. Will update.
P.S. You can visualize the alignment with the bwa-mem using IGV.