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plfjohnson authored Sep 25, 2022
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Expand Up @@ -3,7 +3,7 @@ Contamination estimation from mitochondrial ancient DNA

This repository contains code to generate a R package ("contamMix") that implements a mixture-model used to estimation contamination in ancient mitochondrial DNA using MCMC. The model is detailed in supplementary information 5 ("Likelihood-based method for contamination estimation") of the following paper, which remains the best citation if using this method in a publication:

Fu Q, Mittnik A, Johnson PLF, Bos K, Lari M, Bollongino R, Sun C, Giemsch L, Schmitz R, Burger J, Ronchitelli AM, Martini F, Cremonesi RG, Svoboda J, Bauer P, Caramelli D, Castellano S, Reich D, Pääbo S, and Krause J. (2013). A revised timescale for human evolution based on ancient mitochondrial genomes. Curr Biol, 23:553-9. [doi]
> Fu Q, Mittnik A, Johnson PLF, Bos K, Lari M, Bollongino R, Sun C, Giemsch L, Schmitz R, Burger J, Ronchitelli AM, Martini F, Cremonesi RG, Svoboda J, Bauer P, Caramelli D, Castellano S, Reich D, Pääbo S, and Krause J. (2013). A revised timescale for human evolution based on ancient mitochondrial genomes. *Curr Biol*, 23:553-9. [[doi]](http://dx.doi.org/10.1016/j.cub.2013.02.044)
### Source code context

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The resulting R "source" package then needs to be installed into your R installation (note the filename generated by the above command will depends on the version in the DESCRIPTION file):

R CMD INSTALL contamMix_1.0-10.1.tar.gz
R CMD INSTALL contamMix_1.0-10.tar.gz

Contamination estimation:
1) Generate a FASTA-formatted multiple alignment of potential
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