Computational protocol: A shared MHC supertype motif emerges by convergent evolution in macaques and mice, but is totally absent in human MHC molecules

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Protocol publication

[…] We obtained a multiple sequence alignment of 266 full-length Mamu-B nucleotide sequences from the IPD-MHC database release 1.6.0 (Robinson et al. ). The human allele HLA-B*07:02 was used as an outgroup. From the aligned MHC sequences, we deleted 51 codons encoding residues that form the binding pockets of the MHC molecules in order to avoid binding specificity-determining positions biasing the phylogeny. For phylogenetic reconstruction, we used the maximum-likelihood-based method Phyml (Guindon and Gascuel ) with the HKY model of nucleotide substitution (Hasegawa et al. ), a maximum-likelihood estimate of the proportion of invariable sites, four discrete gamma-distributed substitution rate categories, and 1,000 bootstrap runs. The HKY model was selected based on jModeltest (Posada ). The phylogenetic trees were visualized using SplitsTree (Huson and Bryant ) and Dendroscope (Huson et al. ), respectively. […]

Pipeline specifications

Software tools PhyML, jModelTest, SplitsTree, Dendroscope
Databases IPD-MHC
Application Phylogenetics
Organisms Mus musculus, Macaca mulatta, Homo sapiens
Diseases Acquired Immunodeficiency Syndrome, Infection
Chemicals Glycine