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10 kwi 2012 · Guidelines for measuring, testing and interpreting phylogenetic signal. The results of our sensitivity analysis suggest that Abouheif’s C mean is a well performing method for measuring and testing phylogenetic signal under the set of investigated situations. Similarly, Pagel’s λ performed well for the more complex models of trait evolution ...
19 paź 2016 · Significant results in the standard Mantel test show that the phylogenetic distances are related with the distances based on species traits, but do not distinguish such association from that expected given an evolutionary model of trait evolution.
29 lip 2011 · Given the Euclidean nature of the elementwise square root of phylogenetic distance matrices, the positive semidefinitiveness of the phylogenetic variance–covariance matrix of a trait following a BM model, or related models of trait evolution, can be established.
19 lip 2006 · The BIONJ algorithm results in phylogenies most in accordance with the current NCBI taxonomy, with NJ and FastME performing insignificantly worse, and STC performing as well if applied to high quality distance matrices. δ values are found to be a reliable predictor of phylogenetic accuracy.
Distance-based phylogeny problem. Input: distance matrix of pairwise distances for N species. Goal: find a tree consistent with the distance matrix. This means that the sum of edge lengths connecting each pair of leaves ij corresponds to a distance Mij.
9 mar 2011 · Results. Our results showed that the test has an accurate type I error rate and good power. As expected, power increased with the number of objects (i.e., taxa), the number of partially or completely congruent matrices and the level of congruence among distance matrices. Conclusions.
The K2P model results in a corrected distance, dK2P, given by d K2P = − 1 2 ln(1−2P −Q)− 1 4 ln(1−2Q) where P and Q are the observed fractions of aligned sites whose two bases are related by a transition or transversion mutation, respectively • Notice that the p-distance, p, equals P+Q • The transition/transversion ratio, R, is ...
