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

"We have found Alamut to be an immensely useful tool, and would recommend Alamut to anyone looking for a powerful yet straightforward software program that is able to accurately catalogue and evaluate mutations."

San Francisco, USA



Variant Effect Prediction Training Course



ASHG 2016