# dist.gene

From ape v3.0-2
0th

Percentile

##### Pairwise Distances from Genetic Data

This function computes a matrix of distances between pairs of individuals from a matrix or a data frame of genetic data.

Keywords
manip
##### Usage
dist.gene(x, method = "pairwise", pairwise.deletion = FALSE,
variance = FALSE)
##### Details

This function is meant to be very general and accepts different kinds of data (alleles, haplotypes, SNP, DNA sequences, ...). The rows of the data matrix represent the individuals, and the columns the loci.

In the case of the pairwise method, the distance $d$ between two individuals is the number of loci for which they differ, and the associated variance is $d(L - d)/L$, where $L$ is the number of loci.

In the case of the percentage method, this distance is divided by $L$, and the associated variance is $d(1 - d)/L$.

For more elaborate distances with DNA sequences, see the function dist.dna.

##### Value

an object of class dist. If variance = TRUE an attribute called "variance" is given to the returned object.

##### Note

Missing data (NA) are coded and treated in R's usual way.

dist.dna, cophenetic.phylo, dist