Why is there a difference in nucleotide conservation scores between Alamut Visual and AlamutTM Visual Plus? 

Alamut Visual uses conservation scores from UCSC: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons46way, whereas, AlamutTM Visual Plus uses a more up-to-date set of conservation scores.

• Alamut Visual
  • PhastCons
    • GRCh37 – 46 vertebrates (2013)
    • GRCh38 – 100 vertebrates (2013)
• AlamutTM Visual Plus
  • PhastCons
    • GRCh37 – 100 vertebrates (2018)
    • GRCh38 – 100 vertebrates (2018)