BLAST: provides a variety of custom ViPR databases to identify the most related sequence(s)
Short Peptide Search: allows users to find any peptide sequence using exact, fuzzy, or pattern matching
Sequence Variation Analysis ([Single-nucleotide polymorphism] SNP): calculates sequence variation existing in the specified sequences
Metadata-driven Comparative Analysis Tool for Sequences (Meta-CATS): an automated comparative statistical analysis to identify positions throughout a multiple sequence alignment that significantly differ between groups of sequences possessing specific phenotypic characteristic
Multiple Sequence Alignment: aligns small genomes, gene/protein sequences or large viral genome sequences using one of several algorithm best-suited for the specific job submission
Sequence Alignment Visualization: uses JalView for sequence alignment visualization
Phylogenetic Tree Generation: calculates a tree using one of several available algorithms and evolutionary models
Phylogenetic Tree Visualization: allows the color-coded display of strain metadata on a tree using the Archaeopteryx viewer
GBrowse: provides genome browsing capability for large DNA viral genomes (Herpesviridae and Poxviridae) with integration of ViPR Sequence Features for Vaccinia virus
Sequence Feature Variant Type (SFVT) analysis:[4] provides a centralized repository of functional regions and automatically calculates all observed sequence variation within each defined region
3D Protein Structure Visualization: integrates PDB protein structure files with ViPR Sequence Features when applicable and provides an interactive 3D protein structure viewer using Jmol
Genome Annotator (GATU): allows users to annotate new genome sequences provided by the user
Genotype Determination and Recombination Detection: predicts the genotype for user-provided sequences and identifies possible sites of recombination for viruses in the family Flaviviridae
PCR Primer Design: allows the user to automatically predict ideal primers based on a sequence and specified parameters
ReadSeq: converts between various sequence formats
Sequence Feature Submission Tool: allows users to define a Sequence Feature by filling out a webform
External Analysis Tools: displays a list and description of third-party tools for more specialized analyses
Personal Workbench to save and share data and analysis