Please refer to the Supplementary Methods of the work by a colleague of mine (from Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade)

Kevin

I've helped to develop pVACtools along with some very talented people from the Griffith lab here at WUSTL. It works well

Vaxrank is another, from the Hammerbacher lab

Hello,

You should also check pVACseq (from pVACtools, as mentioned above), MuPeXI and neoepiscope.