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Anymalign   - a multilingual sub-sentential aligner.
Berkeley aligner  
cdec  Chris Dyer - A decoder, aligner, and learning framework for statistical machine translation and other structured prediction models.
fast_align   - a simple, fast, unsupervised word aligner.
GIZA++   - a statistical machine translation toolkit that is used to train IBM Models 1-5 and an HMM word alignment model.
GIZA++ mini-tutorial  
MGIZA++   - is a multi-threaded word alignment tool based on GIZA++, which additionally extends GIZA in other ways by optimizing memory, enabling training interruption and resuming, integrating with Chaski and providing native Windows support.
MTTK : Machine Translation Toolkit