Weka is a collection of machine learning algorithms for data mining tasks. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization. It is also well-suited for developing new machine learning schemes.

You can use weka.classifiers.meta.MultiClassClassifier to use 2-class distribution classifiers (binary classifiers) on multi-class datasets.

Source: Weka FAQ