# all.equal.DNAbin

From ape v4.1
0th

Percentile

##### Compare DNA Sets

Comparison of DNA sequence sets, particularly when aligned.

Keywords
manip
##### Usage
# S3 method for DNAbin
all.equal(target, current, plot = FALSE, ...)
##### Arguments
target, current

the two sets of sequences to be compared.

plot

a logical value specifying whether to plot the sites that are different (only if the labels of both alignments are the same).

further arguments passed to image.DNAbin.

##### Details

If the two sets of DNA sequences are exactly identical, this function returns TRUE. Otherwise, a detailed comparison is made only if the labels (i.e., rownames) of target and current are the same (possibly in different orders). In all other cases, a brief description of the differences is returned (sometimes with recommendations to make further comparisons).

This function can be used for testing in programs using isTRUE (see examples below).

##### Value

TRUE if the two sets are identical; a list with two elements (message and different.sites) if a detailed comparison is done; or a vector of mode character.

image.DNAbin, clustal, checkAlignment, the generic function: all.equal

##### Aliases
• all.equal.DNAbin
##### Examples
# NOT RUN {
data(woodmouse)
woodm2 <- woodmouse
woodm2[1, c(1:5, 10:12, 30:40)] <- as.DNAbin("g")
res <- all.equal(woodmouse, woodm2, plot = TRUE)
str(res)

## if used for testing in R programs:
isTRUE(all.equal(woodmouse, woodmouse)) # TRUE
isTRUE(all.equal(woodmouse, woodm2)) # FALSE

all.equal(woodmouse, woodmouse[15:1, ])
all.equal(woodmouse, woodmouse[-1, ])
all.equal(woodmouse, woodmouse[, -1])

# }
# NOT RUN {
## To run the followings you need internet and Clustal and MUSCLE
## correctly installed.
## Data from Johnson et al. (2006, Science)
refs <- paste("DQ082", 505:545, sep = "")