Kdetrees

[…] el, and among-site rate variation was modeled fitting a gamma distribution with 20 rate categories (+G), as summarized in Table . Similar numbers of “outlier” trees (range 18:22) were detected by the kdetrees-test in the four search types (Table ). However, the distributions of SH-alrt support values are strikingly different for both search algorithms (Wilcoxon, p < 2.2e-16), revealing that gene-t […]

[…] fish 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 is t […]

[…] , aside 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 that these […]