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| Version | Date Released | Status | Release Notes |
| GeneXproTools 4.0 | Jul 17, 2006 | Major Update | Unlimited samples All editions now support an unlimited number of samples. Unlimited variables In the new Enterprise edition. Model Simplification Smaller and simpler models for faster and leaner operation. Excel files support And enhanced database support for easier manipulation of data. |
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| Offline Explorer Enterprise Offline browser (The ability to download up to 100 million URLs per Project) |