theta_estimator | R Documentation |
This function computes the Theta estimator of genetic diversity (Watterson, 1975) while controlling for the presence of gaps in the alignment (Ferretti et al, 2012), frequent in barcoding datasets.
theta_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
Watterson GA , On the number of segregating sites in genetical models without recombination, 1975, Theor. Popul. Biol.
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.
pi_estimator
delineate_phylotypes
data(woodmouse) alignment <- as.character(woodmouse) # nucleotidic alignment theta_estimator(alignment)
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