moire

Summary sheet

Main use-cases	Estimating multiplicity of infection (MOI), population allele frequencies, and within-host relatedness from polyallelic genomics data.
Authors	Maxwell Murphy, Bryan Greenhouse
Latest version	v3.5.0
License	GNU General Public License v3.0
Website	https://eppicenter.github.io/moire
Code repository	https://github.com/eppicenter/moire
Publication	https://doi.org/10.1093/bioinformatics/btad245
Tutorial authors	Kathryn Murie, Maxwell Murphy
Tutorial date	7-Jan-25

Purpose

The moire (Multiplicity Of Infection and allele frequency REcovery) tool can be used to estimate allele frequencies, MOI, and within-host relatedness from genetic data subject to experimental error. It utilises a Markov Chain Monte Carlo (MCMC) based approach to Bayesian estimation and can take both polyallelic and SNP data as inputs. This tool also introduces a new metric called effective MOI (eMOI), which combines MOI and within-host relatedness into a unified and comparable measure of genetic diversity.

Existing resources

• The moire website provides basic usage instructions
• Within the moire website there is a more in depth tutorial using simulated genotyping data.

Citation

citation('moire')

To cite package 'moire' in publications use:

  Murphy M, Greenhouse B (2024). "MOIRE: A software package for the
  estimation of allele frequencies and effective multiplicity of
  infection from polyallelic data." _Bioinformatics_.
  doi:10.1093/bioinformatics/btae619
  <https://doi.org/10.1093/bioinformatics/btae619>.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {MOIRE: A software package for the estimation of allele frequencies and effective multiplicity of infection from polyallelic data},
    author = {Maxwell Murphy and Bryan Greenhouse},
    journal = {Bioinformatics},
    year = {2024},
    month = {oct},
    doi = {10.1093/bioinformatics/btae619},
  }