Kdetrees

[…] model. fasttree was compiled with double-precision enabled for maximum accuracy (see the manual for details). the resulting gene trees are screened to detect “outliers” with help of the r package kdetrees (v.0.1.5) (weyenberg et al., , ). it implements a non-parametric test based on the distribution of tree topologies and branch lengths expected under the multispecies coalescent, identifying […]

[…] included as an out-group, scyliorhinus canicula, leucoraja erinacea and callorhinchus milii., analysis was performed ignoring pendant edge lengths. a total of 97 outlying trees were removed using kdetrees (), so that 1193 gene trees remained. the fréchet mean was computed using the bačák algorithm and its topology is shown in . the mean tree does not resolve whether coelacanth or lungfish […]

[…] from the position of the primary misannotated species. fig. 8. , given the “outlier” nature of the loci identified in the small cluster, we also applied a specialized outlier detection package, kdetrees (). remarkably, with geodesic distances, it identified the exact same 37 loci as outliers (supplementary fig. s9, supplementary material online). this provides additional evidence […]