This looks like a false positive by the Gateway Anti-Virus. I've just rechecked both the Windows and the Linux/OS X versions of DeNovoGUI (and also manually verified the content) and I don't find any evidence for the reported Trojan virus. Could you check with a different anti-virus software?
Best regards,
Harald
PS: In order to avoid duplicated comments on this issue, please refer to the issue tracker for future messages: https://github.com/compomics/denovogui/issues/38