pi_estimator: Compute nucleotidic diversity (Pi estimator)

In RPANDA: Phylogenetic ANalyses of DiversificAtion

Compute nucleotidic diversity (Pi estimator)

Description

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.

Usage

pi_estimator(sequences)

Arguments

sequences

a matrix representing the nucleotidic alignment of all the sequences present in the phylogenetic tree.

Value

An estimate of genetic diversity

Author(s)

Ana C. Afonso Silva & Benoît Perez-Lamarque

References

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.

See Also

theta_estimator delineate_phylotypes

Examples

data(woodmouse)

alignment <- as.character(woodmouse) # nucleotidic alignment 

pi_estimator(alignment)

RPANDA documentation built on Oct. 24, 2022, 5:06 p.m.