Genetic Relatedness Between Polyclonal Infections
Calculate Allele Frequencies
Read and Reformat Data
Grid of Parameter Values
Calculate COI
Likelihood for ,
Pairwise Relatedness
Estimate Relatedness and a Number of Related Strains
Relatedness Between Two Samples
Logarithms of reval
Match Samples and Allele Frequencies
Combine two matrices
Colorbar
Plot Relatedness Estimates
An implementation of Dcifer (Distance for complex infections: fast estimation of relatedness), an identity by descent (IBD) based method to calculate genetic relatedness between polyclonal infections from biallelic and multiallelic data. The package includes functions that format and preprocess the data, implement the method, and visualize the results. Gerlovina et al. (2022) <doi:10.1093/genetics/iyac126>.