pofadinr R package
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README.md

README.md

pofadinr

Distance methods from SNP data

This is the repository for the pofadinr R package

About

The pofadinr R package implements the distances genpofad and matchstates based on single nucleotide polymorphisms (Joly et al. 2015). They were developped to take into account intra-individual polymorphisms when estimating genetic distances between individuals. genpofad, in particular, provides an accurate measure of genetic distance and is useful to deal with hybrids and individuals of different ploidy levels.

Installation

Manual installation

Download either the source files or the binaries for the latest release and install them in R.

Direct installation in R

You first need to install the devtools package.

$> install.packages("devtools")

And then, intall the pofadinr package from the github repository.

$> library(devtools)

$> install_github("simjoly/pofadinr")

Source and binaries

Check the latest release.

Notes

This package was written to make available in R some SNP based distance methods (Joly et al. 2015). However, more methods are available in the POFAD software.

Note that this implementation is much faster than that of the POFAD program. This is because pofadinr uses bit-wise operations for comparing nucleotides, following the bit-level coding scheme for nucleotides developped by Emmanuel Paradis.

References

Joly, S., Bryant, D. and Lockhart, P.J. 2015. Flexible methods for estimating genetic distances from nucleotide data. Methods in Ecology and Evolution, 6, 938–948.