pi_estimator | R Documentation |
This function computes the Pi estimator of genetic diversity (Nei and Li, 1979) while controlling for the presence of gaps in the alignment (Ferretti et al, 2012), frequent in barcoding datasets.
pi_estimator(sequences)
sequences |
a matrix representing the nucleotidic alignment of all the sequences present in the phylogenetic tree. |
An estimate of genetic diversity
Ana C. Afonso Silva & Benoît Perez-Lamarque
Nei M & Li WH, Mathematical model for studying genetic variation in terms of restriction endonucleases, 1979, Proc. Natl. Acad. Sci. USA.
Ferretti L, Raineri E, Ramos-Onsins S. 2012. Neutrality tests for sequences with missing data. Genetics 191: 1397–1401.
Perez-Lamarque B, Öpik M, Maliet O, Silva A, Selosse M-A, Martos F, and Morlon H. 2022. Analysing diversification dynamics using barcoding data: The case of an obligate mycorrhizal symbiont, Molecular Ecology, 31:3496–512.
theta_estimator
delineate_phylotypes
data(woodmouse)
alignment <- as.character(woodmouse) # nucleotidic alignment
pi_estimator(alignment)
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