MALT is a sequence aligner especially designed for metagenomics. When provided with MEGAN mapping files, MALT applies LCA and produces RMA6 files ready to open with MEGAN.
MALT deals both with protein and DNA alignments. But in order to build an index from the database. The index building step is when you should provide the mapping files.
Please use this category to solve any problems with MALT and share your suggestions.
MALT can be downloaded here.
Comprehensive MALT manual is available here,
and a MALT paper here