multidna2alignment | R Documentation |
The functions multidna2alignment
and multiphyDat2alignment
concatenates separate sequences and return an alignment object of the seqinr package.
multidna2alignment(x, genes = TRUE)
multiphyDat2alignment(x, genes = TRUE)
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. |
a alignment object
Thibaut Jombart t.jombart@imperial.ac.uk, Zhian N. Kamvar, Klaus Schliep
concatenate
as.alignment
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 <- multidna2alignment(x)
y
x2 <- multidna2multiphyDat(x)
z <- multiphyDat2alignment(x2)
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