mdendro (version 2.3.0)

mfnj: MultiFurcating Neighbor-Joining

Description

A MultiFurcating version of the Neighbor-Joining method for reconstructing phylogenetic trees (Fernandez et al., 2023). Multifurcated phylogenetic trees can group more than two clusters when tied distances occur, and therefore they do not depend on the order of the input taxa.

Usage

mfnj(x, digits = NULL)

Value

An object of class "mfnj" that describes the multifurcated phylogenetic tree obtained. The object is a list with the following components:

call

The call that produced the result.

digits

Number of significant decimal digits used as precision. It is given by the user or automatically set to the number of significant decimal digits in the input distances.

size

Number of taxa.

labels

Labels of the taxa.

nwk

A string describing the output phylogenetic tree in Newick format.

polytomies

Number of polytomies in the phylogenetic tree.

Class "mfnj" has methods for the following generic functions:

print, summary and plot.

Arguments

x

A structure of class "dist" containing non-negative distances.

digits

An integer value specifying the precision, i.e., the number of significant decimal digits to be used for the comparisons between distances. This is an important parameter, since equal distances at a certain precision may become different by increasing its value. Thus, it may be responsible of the existence of tied distances. If the value of this parameter is negative or NULL (default), then the precision is automatically set to that of the input distance with the largest number of significant decimal digits.

Author

Alberto Fernandez and Sergio Gomez .

References

Fernandez, A.; Segura-Alabart, N.; Serratosa, F. (2023). The MultiFurcating Neighbor-Joining algorithm for reconstructing polytomic phylogenetic trees. Journal of Molecular Evolution, 91, 773--779. <doi:10.1007/s00239-023-10134-z>.

Randi, E.; Gentile, L.; Boscagli, G.; Huber, D.; Roth, H.U. (1994). Mitochondrial DNA sequence divergence among some west European brown bear (Ursus arctos L.) populations. Lessons for conservation. Heredity, 73(5): 480--489. <doi:10.1038/hdy.1994.146>.

See Also

dist.

Examples

## Table 4 from Randi et al. (1994)
m <- matrix(0, 9, 9)
m[lower.tri(m)] <- c(1.3, 4.3, 4.3, 2.7, 3.0, 1.7, 2.0,  8.7,
                          4.3, 4.3, 2.3, 3.0, 1.7, 2.0,  8.0,
                               0.7, 5.0, 1.3, 2.7, 3.0, 10.0,
                                    5.0, 1.3, 2.7, 3.0, 10.0,
                                         3.7, 2.3, 2.7, 10.0,
                                              2.0, 2.3,  8.7,
                                                   0.3,  9.0,
                                                         9.4)
x <- as.dist(m)
attr(x, "Labels") <- c("Abruzzo", "Pyrenees", "Kodiak", "Captive-3",
                       "Captive-4", "Captive-5", "Grizzly", "Polar-2", "Black")

## Reconstruct neighbor-joining phylogenetic tree
t <- mfnj(x, digits = 6)
summary(t)
plot(t)