Alamut Visual

Features of Alamut® Visual

Alamut® Visual, the reference software for human variation interpretation


  • Gene browser supporting human genes (protein coding, non-protein coding and pseudogenes)
  • A single user interface with relevant annotations gathered from public databases such as NCBI, EBI, UCSC
  • HGVS nomenclature compliant software
  • Mutation reporting with pathogenicity clues
  • Calculates functional impact of variants with relevant prediction tools:
    • Splicing prediction tools (SpliceSiteFinder-like, MaxEntScan, NNSPLICE, GeneSplicer, Human Splicing Finder)
    • ESE tools
    • Missense prediction tools (Align GVGD, SIFT, MutationTaster, PolyPhen-2, KD4v)
  • Advanced BAM NGS alignments viewer with VCF support


  • Automatically connects to the well-curated Alamut software suite database
  • Manages and visualizes lab’s variants
  • Automatic form filling of web-based missense prediction tools
  • Mutation-focused search engine over PubMed abstracts
  • Manages and visualizes sequence-based private annotations (e.g. primers, probes)
  • Uses standard bioinformatics file formats (e.g., VCF, BAM, BED, GFF)


  • Nucleotide conservation (phastCons and phyloP scores)
  • Reference transcripts
  • dbSNP, ExAC, ESP/EVS variants
  • Genome of the Netherlands (GoNL), Japan Human Genetic Variation Database (HGVD)
  • ClinVar, SwissProt pathogenic variants
  • COSMIC variants (available at no extra cost to both academic and commercial users — users who wish to download the COSMIC database, manipulate or mine it directly would need to obtain it from the Sanger Institute)
  • Integrates HGMD® Professional (requires a separate subscription from QIAGEN)
  • Functional protein domains
  • Orthologues alignments
  • Links to external locus-specific databases


Alamut Visual complies with the ACMG/AMP Variant Interpretation Standards and Guidelines. Click here for details.

Alamut Visual screenshot

What they say
about Alamut Visual

"Alamut is the best tool I have used for the annotation of DNA variants. It has a great user interface, combines data from multiple sources and allows for ease of variant interpretation by clinical geneticists."

Mt. Sinai Hospital, Toronto



Variant Effect Prediction Training Course



ASHG 2016