NJ: Neighbor-Joining
In KlausVigo/phangorn: Phylogenetic Reconstruction and Analysis
NJ R Documentation
Neighbor-Joining
Description
This function performs the neighbor-joining tree estimation of Saitou and
Nei (1987). UNJ is the unweighted version from Gascuel (1997).
Usage
NJ(x)
UNJ(x)
Arguments
x
A distance matrix.
Value
an object of class "phylo".
Author(s)
Klaus P. Schliep klaus.schliep@gmail.com
References
Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new
method for reconstructing phylogenetic trees. Molecular Biology and
Evolution, 4, 406–425.
Studier, J. A and Keppler, K. J. (1988) A Note on the Neighbor-Joining
Algorithm of Saitou and Nei. Molecular Biology and Evolution,
6, 729–731.
Gascuel, O. (1997) Concerning the NJ algorithm and its unweighted version,
UNJ. in Birkin et. al. Mathematical Hierarchies and Biology,
149–170.
See Also
nj, dist.dna,
dist.hamming, upgma,
fastme
Examples
data(Laurasiatherian)
dm <- dist.ml(Laurasiatherian)
tree <- NJ(dm)
plot(tree)
KlausVigo/phangorn documentation built on Nov. 20, 2024, 12:47 p.m.
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| NJ | R Documentation |
Neighbor-Joining
Description
This function performs the neighbor-joining tree estimation of Saitou and Nei (1987). UNJ is the unweighted version from Gascuel (1997).
Usage
NJ(x)
UNJ(x)
Arguments
x |
A distance matrix. |
Value
an object of class "phylo".
Author(s)
Klaus P. Schliep klaus.schliep@gmail.com
References
Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4, 406–425.
Studier, J. A and Keppler, K. J. (1988) A Note on the Neighbor-Joining Algorithm of Saitou and Nei. Molecular Biology and Evolution, 6, 729–731.
Gascuel, O. (1997) Concerning the NJ algorithm and its unweighted version, UNJ. in Birkin et. al. Mathematical Hierarchies and Biology, 149–170.
See Also
nj, dist.dna,
dist.hamming, upgma,
fastme
Examples
data(Laurasiatherian)
dm <- dist.ml(Laurasiatherian)
tree <- NJ(dm)
plot(tree)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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