pi_estimator

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.

Implements macroevolutionary analyses on phylogenetic trees. See
Morlon et al. (2010) <DOI:10.1371/journal.pbio.1000493>, Morlon et al. (2011)
<DOI:10.1073/pnas.1102543108>, Condamine et al. (2013) <DOI:10.1111/ele.12062>,
Morlon et al. (2014) <DOI:10.1111/ele.12251>, Manceau et al. (2015) <DOI:10.1111/ele.12415>,
Lewitus & Morlon (2016) <DOI:10.1093/sysbio/syv116>, Drury et al. (2016) <DOI:10.1093/sysbio/syw020>,
Manceau et al. (2016) <DOI:10.1093/sysbio/syw115>, Morlon et al. (2016) <DOI:10.1111/2041-210X.12526>, Clavel & Morlon (2017) <DOI:10.1073/pnas.1606868114>,
Drury et al. (2017) <DOI:10.1093/sysbio/syx079>, Lewitus & Morlon (2017) <DOI:10.1093/sysbio/syx095>,
Drury et al. (2018) <DOI:10.1371/journal.pbio.2003563>, Clavel et al. (2019) <DOI:10.1093/sysbio/syy045>, Maliet et al. (2019) <DOI:10.1038/s41559-019-0908-0>,
Billaud et al. (2019) <DOI:10.1093/sysbio/syz057>, Lewitus et al. (2019) <DOI:10.1093/sysbio/syz061>,
Aristide & Morlon (2019) <DOI:10.1111/ele.13385>, Maliet et al. (2020) <DOI:10.1111/ele.13592>, Drury et al. (2021) <DOI:10.1371/journal.pbio.3001270>,
Perez-Lamarque & Morlon (2022) <DOI:10.1111/mec.16478>, Perez-Lamarque et al. (2022) <DOI:10.1101/2021.08.30.458192>, Mazet et al. (2023) <DOI:10.1111/2041-210X.14195>, Drury et al. (2024) <DOI:10.1016/j.cub.2023.12.055>.

H<c3><a9>l<c3><a8>ne Morlon

RPANDA

Phylogenetic ANalyses of DiversificAtion

Hélène Morlon

Eric Lewitus

Fabien Condamine

Marc Manceau

Julien Clavel

Jonathan Drury

Olivier Billaud

Odile Maliet

Leandro Aristide

Benoit Perez-Lamarque

Nathan Mazet

pi_estimator function

<dl>
<dt>sequences</dt>
<dd>a matrix representing the nucleotidic alignment of all the sequences present in the phylogenetic tree.</dd>
</dl>

Arguments

Ana C. Afonso Silva &amp; Benoît Perez-Lamarque

Author

Compute nucleotidic diversity (Pi estimator) — pi_estimator

<dl>


<dt>sequences</dt>
<dd>a matrix representing the nucleotidic alignment of all the sequences present in the phylogenetic tree.</dd>


</dl>

Compute nucleotidic diversity (Pi estimator)

pi_estimator: Compute nucleotidic diversity (Pi estimator)

Description

Usage

Value

Arguments

Author

References

See Also

Examples