Alamut® 2.0 is a decision-support software application for medical molecular genetics, dedicated to mutation diagnostics. By integrating gene annotations from multiple data sources and in silico prediction tools in a consistent environment, the software helps increase quality and productivity of variants assessment. This latest version includes a number of new features and user-defined custom tools. Alamut now supports the GRCh37 (hg19) genome assembly as well as RefSeqGene and Locus Reference Genomic sequences. It integrates the Human Gene Mutation Database, available to HGMD® Professional subscribers. It provides automatic computation of missense predictions with PolyPhen-2, SIFT, and Align GVGD. The splicing prediction toolset has been enriched with the Human Splicing Finder prediction algorithm. A new conservation score across vertebrate genomes, phyloP, has also been added.