Can’t sign in to FlowJo™ or SeqGeq™ Software?

FlowJo Portal login window with the FlowJo Desktop Application

 In some cases, your institution’s network security settings may prevent FlowJo and SeqGeq from connecting to FlowJo Portal. If you are able to sign in to your FlowJo Portal account page, but can’t sign in to FlowJo/SeqGeq, we suggest the following: 

  1. Contact your institution’s IT Department.
  2. Request that your IT department change your network security settings to allow FlowJo and/or SeqGeq to pass SSL certifications to pass by the network security settings. The servers respective URLs are below. FlowJo uses ports 80 and 443.
  3. I would also suggest inquiring with your IT security group if they use a Proxy. If so, the proxy information they provide can be entered within the FlowJo License Preferences.
  4. Once resolved, you should be able to sign in to FlowJo/SeqGeq! If you continue to have issues with login, please contact and

 IT Dept. Special Instructions

The new FlowJo Portal licensing system authorizes FlowJo over SSL and the application requires the SSL cert from our certificate authority. Some high security networks are setup to replace SSL certs with internal certs. If this is the case, FlowJo will not authenticate properly. To resolve this, change the network security settings to allow FlowJo and/or SeqGeq to pass SSL certs to the application. Please see the respective URLs and instructions above.