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)
  • Access to the CentoMD® Variant Database (a separate subscription from Centogene is required)
  • 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 are very grateful for the work you do with Alamut and continuing to improve it. We use it on daily basis to help us interpret variants for clinical tests including our technicians, analysts, genetic counselors and lab directors. Alamut has the comprehensive information available for interpreting variants and great documentation. I’ve recommended Alamut to many customers who ask me about the tools that I use. Many thanks to you for making this possible."

Cincinnati Children's Hospital Medical Center



ACMG 2017



Variant Effect Prediction Training Course