Hi,
There is No Open Source software app for molecular biology. The main ones: Geneious, SnapGene and Benchling offer some free very limited functionality versions. None is powerful enough and more importantly none of them can be extended with new required functionality.
Is there interest in creating one?
While toying with the idea I developed a functional proof of concept intended for now to illustrate and verify PCR and LAMP reactions using real sequences and steps. None of the commercial software offers that. Geneious can be extended to do that but the license is quite expensive.
I used BioPython library but BioJava is another option.
Take a look at Ottawa Bio Science - Ottawa's Community Biology Group for an image of the current working prototype as posting images here seem not to work.