• CDC (Center for Disease Control)
• WHO (World Health Organization)
• OFFLU (OIE/FAO)

• NCBI Influenza Virus Resources
• FluDB
• BGI Influenza Virus Database
• GISAID EpiFlu^TM Database (login required)

• Influenza vaccine strain selection (CDC)
• Historical annual reformulations of the influenza vaccine (Wikipedia)
• Influenza Virus Vaccine Composition and Lot Release (FDA)

• Influenza Primer Design Resource (fludb.org)
• Primer Hunter (a tool for selecting highly sensitive and specific primers for virus subtyping)
• Universal Primer Set (Journal Article)
• Primer 3 (general primer design)

• NCBI Influenza Virus Sequence Annotation Tool
• Sequence batch annotation (fludb.org)
• ORF finder at NCBI

• Bioinformatics used for RNA Sequencing analysis. Useful if you want to see the genetic differences between samples or compare the sample.
• Article detailing the whole RNA Sequencing process
• Download Tophat
• Download Cufflinks
• Download CumbeRbund
• Location of GTF and BWT/BWT2 files for use with Tuxedo Suit

• Epitope Informatics
• Epitope Search at FluDB.org
• ImmunoGRID Database
• Immune Epitope Database and Analysis Resource

• BEAST
• GARLI
• HYPHY
• MrBayes
• PAUP*
• TNT

A complete list of phylogenetic programs is available at Dr. Joe Felsenstein's collection.

• MUSCLE
• CLUSTAL

A complete list of multiple sequence alignment program is available at Wikipedia.

• DFprot (webtool for predicting local chain deformability)
• elNémo (a elastic network model analysis webserver)
• WEBnm@ (automated computation and analysis of low-frequency normal modes for proteins)

Only several normal mode analysis tools are listed. Collection of protein structural modeling and visualization tools at digbio laboratory at University of Missouri

• mFold (RNA secondary structure prediction at Rensselaer Polytechnic Institute)
• RFold (An exact algorithm for computing local base pairing probabilities)
• Rnall (for RNA local secondary structure prediction)
• RnallViewer (visualization of RNA secondary structure predicted by Rnall)
• Vienna and RNAWebserver (RNA secondary structure prediction at Vienna)

A complete list is available at Wikipedia.