Computes a minimum spanning tree using Kruskal's algorithm, the minimum spanning network using Bandelt et al.'s algorithm, or the randomized minimum spanning tree (Paradis 2017).
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a distance matrix, either as an object of class
number of randomizations.
an object of class
ape has a function named
mst which is older (and used by
other packages) and returns its results in a different form. The
present version is more efficient. If you want to use the older
version after loading pegas, use
ape::mst since ape
will certainly always be loaded before pegas.
Bandelt, H. J., Forster, P. and Rohl, A. (1999) Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16, 37–48.
Kruskal, J. B., Jr. (1956) On the shortest spanning subtree of a graph and the traveling salesman problem. Proceedings of the American Mathematical Society, 7, 48–50.
Paradis, E. (2018) Analysis of haplotype networks: the randomized minimum spanning tree method. Methods in Ecology and Evolution, 9, 000–000. DOI: 10.1111/2041-210X.12969.
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Loading required package: ape Loading required package: adegenet Loading required package: ade4 /// adegenet 2.0.1 is loaded //////////// > overview: '?adegenet' > tutorials/doc/questions: 'adegenetWeb()' > bug reports/feature requests: adegenetIssues() Attaching package: 'pegas' The following object is masked from 'package:ade4': amova The following object is masked from 'package:ape': mst Haplotype network with: 15 haplotypes 14 links 0 alternative links link lengths between 2 and 14 steps Use print.default() to display all elements.
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