malaria.em

Author

Nicholas Hathaway/Shazia Ruybal-Pesántez

Published

July 11, 2025



Summary sheet

Main use-cases estimate haplotype frequencies
Authors Xiaohong Li
Latest version 2025-01-26
Code repository https://github.com/PlasmoGenEpi/malaria.em
Publication https://doi.org/10.2202/1544-6115.1321

Purpose

Program designed to discern the combinations of mutations at the population level to estimate frequencies of these clonal sequences. This program utilizes an expectation maximization (EM) approach to maximum likelihood estimation of haplotype frequencies from the SNP loci per sample information.

The code for this program was removed from CRAN in 2014 and does not appear to be actively maintained (CRAN archive). However, we have fixed some bugs in a newer version, and it is now available through the PlasmoGenEpi GitHub repository.

Citation

(Li et al. 2007)

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References

Li, Xiaohong, Andrea S Foulkes, Recai M Yucel, and Stephen M Rich. 2007. “An Expectation Maximization Approach to Estimate Malaria Haplotype Frequencies in Multiply Infected Children.” Stat. Appl. Genet. Mol. Biol. 6 (November): Article33.