Sequence Alignment Visualization: uses JalView for sequence alignment visualization
Phylogenetic tree construction: calculates a tree using various algorithms and evolutionary models
Phylogenetic Tree Visualization: allows the color-coded display of strain metadata on a tree generated with one of several available algorithms and/or evolutionary models and viewed with Archaeopteryx
3D Protein Structure Visualization: integrates PDB protein structure files with sequence conservation score and IRD Sequence Features and provides an interactive 3D protein structure viewer using Jmol
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
Metadata-driven Comparative Analysis Tool for Sequences (Meta-CATS): an automated comparative statistical analysis to identify positions that significantly differ between user-defined sequence groups
Sequence Variation Analysis (SNP): pre-computed sequence variation analysis in all IRD sequences; also allows users to calculate the extent of sequence variation in user-specified sequences
PCR Primers/Probes: provides a repository of commonly used primers for influenza virus identification, and calculates the polymorphisms of all related IRD sequences at the primer positions
PCR Primer Design: allows PCR primer design for IRD and user-provided sequences
Sequence annotation: determines the user-provided nucleotide sequence's influenza type, segment number and subtype (for segments 4 and 6), and translates the nucleotide sequence
HPAI H5N1 Clade Classification: predicts the clade of highly pathogenic H5 HA sequences
ReadSeq: converts between various sequence formats
Data Submission Tool: allows users to submit influenza sequences, Sequence Features, and experimental data online
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
^Squires, R.B., Noronha, J., Hunt, V., et al. Influenza Research Database: an integrated bioinformatics resource for influenza research and surveillance. Influenza Other Respi Viruses. (2012) 6(6): 404–416.
doi:10.1111/j.1750-2659.2011.00331.x
^Squires B., Macken C., Garcia-Sastre A. et al. BioHealthBase: informatics support in the elucidation of influenza virus host-pathogen interactions and virulence. Nucleic Acids Res. (2008) 36 (suppl 1): D497-D503.
doi:10.1093/nar/gkm905
^
abNoronha, J.M., Liu, M, Squires, R.B., et al. Influenza Sequence Feature Variant Type (Flu-SFVT) analysis: evidence for a role of NS1 in influenza host range restriction. J Virol. (2012) 86(10): 5857-5866.
doi:10.1128/JVI.06901-11