c.alignment: Concatenation of DNA Sequences

In fmichonneau/phyloch: Tools for phylogenetics and taxonomy

Description

c.alignment concatenates two or more sets of sequences of the same gene partition into a single object of class alignment.

c.genes concatenates two or more sets of sequences representing different gene partitions.

Usage

## S3 method for class 'alignment'
c(...)

## S3 method for class 'genes'
c(..., single.list, match = TRUE)

Arguments

...	two or more object of class alignment or DNAbin separated by commas.
single.list	list object whose elements are of class DNAbin
match	logical, if match = TRUE only those sequences present in all partitions will be concatenated; if match = FALSE the concatenated alignment will contain all sequences.

Value

An object of classes alignment or codeDNAbin.

Note

Sequences are matched by their named, therefore sequence names require identical spelling if they are to be concatenated.

Author(s)

Christoph Heibl

See Also

read.fas and write.fas for reading and writing DNA sequence files.

Examples

# examples for c.genes
# --------------------

data(woodmouse)
w1 <- woodmouse[, 1:250]
w2 <- woodmouse[, 251:750]
w3 <- woodmouse[, 751:965]

w <- c.genes(w1, w2, w3)

w.list <- list(w1, w2, w3)
W <- c.genes(single.list = w.list)

identical(w, W)

fmichonneau/phyloch documentation built on May 16, 2019, 1:45 p.m.