@article{fdi:010072846,
  title = {{A}nalysis of haplotype networks : the randomized minimum spanning tree method},
  author = {{P}aradis, {E}mmanuel},
  editor = {},
  language = {{ENG}},
  abstract = {1. {H}aplotype network construction is a widely used approach for analysing and visualizing the relationships among {DNA} sequences within a population or species. {T}his approach has some problems such as how to quantify alternative links among sequences or how to plot efficiently networks to compare them easily. 2. {I}n this paper, a new method is presented: the randomized minimum spanning tree method, based on randomizing the input order of the data in order to produce alternative branchings in the haplotype network. {I}t is shown that this new method can produce, at least in some situations, networks with less alternative links than the minimum spanning network method. 3. {A} new graphical display of haplotype networks is introduced here. {T}his is based on calculating the coordinates of the haplotypes from a multidimensional scaling of the haplotype distance matrix. {T}he display can be done in two or three dimensions. {T}he eigenvalues extracted from the multidimensional scaling analysis give an indication of the relevant number of dimensions. 4. {T}hese tools are illustrated with the analyses of published data on the leopard and on the jaguar. {T}hese analyses show interesting and contrasting patterns between these two species of big cats. 5. {A}ll tools are implemented in {R} and available in the package pegas.},
  keywords = {{H}amming distance ; haplotype network ; microevolution ; minimum spanning ; tree ; {P}anthera},
  booktitle = {},
  journal = {{M}ethods in {E}cology and {E}volution},
  volume = {9},
  numero = {5},
  pages = {1308--1317},
  ISSN = {2041-210{X}},
  year = {2018},
  DOI = {10.1111/2041-210x.12969},
  URL = {https://www.documentation.ird.fr/hor/fdi:010072846},
}