GASiC
Genome Abundance Similarity Correction
...GASiC is a method to correct read alignment results for the ambiguities imposed by similarities of genomes. It has superior performance over existing methods.
You can find the accompanying paper here:
http://nar.oxfordjournals.org/content/41/1/e10.short
Thanks to the great work of the SeqAn team, you can now use GASiC as a Knime workflow:
https://github.com/seqan/knime_seqan_workflows/tree/master/metagenomics_gasic_workflow