Table 2 In silico analysis - bioinformatic tools and databases

NetMHCpan

http://www.cbs.dtu.dk/services/NetMHCpan/

A server for predicting the binding of peptide sequences to MHC molecules (class I) for humans and other species

NetMHCIIpan

http://www.cbs.dtu.dk/services/NetMHCIIpan/

A server for predicting the binding of peptide sequences to MHC molecules (class II) for humans and other species

Immune Epitope Database (IEDB)

http://www.immuneepitope.org/

A database storing data related to antibody and T-cell epitopes for humans, non-human primates, rodents, and other animal species

Allele Frequency Net Database (AFND)

http://www.allelefrequencies.net/

A database storing allele, haplotype and genotype frequencies in worldwide populations, sourced from over 1,200 studies, concerning immune-related genes (HLA, KIR, MIC and cytokine gene polymorphisms)

PyPop

http://www.pypop.org/

Open-source software package for the analysis of populations at large scale and multiple loci

GraphViz

http://www.graphviz.org/

Open source graph visualization software

dbMHC

http://www.ncbi.nlm.nih.gov/gv/mhc/main.cgi?cmd=init

A database providing DNA, protein and clinical data related to the human major histocompatibility complex (MHC)

PHYLIP

http://evolution.genetics.washington.edu/phylip.html

Open source software for inferring phylogenies

TreeView

http://taxonomy.zoology.gla.ac.uk/rod/treeview.html

Open source tree viewing software