multidna2genind: Convert multidna into genind
In apex: Phylogenetic Methods for Multiple Gene Data

Description Usage Arguments Value Author(s) See Also Examples

The functions multidna2genind and multiphyDat2genind concatenates separate DNA alignments, and then extracts SNPs of the resulting alignment into a genind object.

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multidna2genind(x, genes = TRUE, mlst = FALSE, gapIsNA = FALSE)

multiphyDat2genind(x, genes = TRUE, mlst = FALSE, gapIsNA = FALSE)

`x`	a multidna or multiphyDat object.
`genes`	an optional vector indicating the genes to retain for the concatenation; any way to subset the list in x@dna or x@seq is acceptable; by default, all genes are used.
`mlst`	if `TRUE`, each gene will result in a single locus in the genind object. (Default to `FALSE`)
`gapIsNA`	if `TRUE` and `mlst = TRUE`, sequences that consist entirely of gaps will be considered as NAs. (Default to `FALSE`)

a genind object

Thibaut Jombart t.jombart@imperial.ac.uk, Zhian N. Kamvar, Klaus Schliep

concatenate
DNAbin2genind to convert single DNAbin objects.

## simple conversion with nicely ordered output
data(woodmouse)
genes <- list(gene1=woodmouse[,1:500], gene2=woodmouse[,501:965])
x <- new("multidna", genes)
x
y <- multidna2multiphyDat(x)
y
z1 <- multidna2genind(x)
z1
z2 <- multiphyDat2genind(y)
all.equal(z1, z2)