This package contains two perl scripts and corresponding distance matrixes to calculate amino acid sequence divergence among alleles in a pairwise manner or among all alleles of an individual. The scripts were specifically written to calculate divergence between alleles of MHC/HLA immune genes.
Written by Tobias Lenz, last updated May 2020.
Please cite the following reference when using this script in your research:
Pierini & Lenz (2018) Divergent allele advantage at human MHC genes: signatures of past and ongoing selection. Molecular Biology and Evolution 35: 2145-2158. https://doi.org/10.1093/molbev/msy116
Features
- Simple calculation of individual allele divergence at MHC/HLA genes
- Different distance parameters available, including Grantham and pdistance
- Works for any species when sequence data is available
- Sequence alignments for human HLA class I and class II alleles included
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