These are different product sets with a little overlap.
Gentran is an Edi Partner Manager with the ability to transform data from any Edi standard to a flat file format. It provides the connect layer to the VAN. Its ability around XML appears poor.
Mercator is purely a data transformation engine that can deal with any data format but doesn't do the Partner Management or the seamless connectivity to VAN's without add on products.
Its a few years since I looked at Gentran in any detail, it may have moved on.
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