Finding common and different genes between species

Question

[Ric]

Hi, We have two plants which one of them is the wild type. For each of them, I used the Scallop results with TransDecoder. How is possible to determine which are common and different genes between those two plants from Scallop/Transdecoder results?

Thank you in advance,

[ashish]

Are these plants related? You may look at presence/absence variation tools. These are part of pangenome/transcriptome analysis methods. Here is one approach.