MALLET is much easier to use and does most of its work unnoticed. You also do not need to convert the format to anything, you just give it text files and this gives you the results.
Weka requires converting text to a specific format (Weka script is so slow and inefficient for this that I would recommend you write your own).
The problem with MALLET is that the training uses GB of memory, and this can take several hours if you have large training sets.
Weka has more documentation, but most of them make no sense. MALLET has very little documentation, but is very easy to use.
Honestly, after testing both of them, I decided to write my own classifier.
Alasdair
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