PairwiseAlignPanel running out of heap space

Java runs out of heap space when performing a pairwise alignment of 340 sequences or more, seemingly due to creating too many AlignSeq objects.

Is there a way to get around this?
I have tried initialising an AlignSeq prior to the main loop and re-using the object with its seqInit method. This makes it incredibly slow and it was not able to finish this in any feasible time. I have also tried splitting the Alignment internally into smaller groups, align those and all combinations of them to not have one big PairwiseAlignPanel, but that only crashed during the 340th.