By which methods can we evaluate the reliability of a phylogenetic tree?
['For robustness evaluation, we apply bootstrap and jackknife techniques to input data.', 'An alignment confidence score capturing robustness to guide tree uncertainty.', 'We build on the widely used bootstrap method for perturbing the phylogenetic tree.', 'SuperTRI: A new approach based on branch support analyses of multiple independent data sets for assessing reliability of phylogenetic inferences.', 'To overcome these limitations, we propose a new approach, called SuperTRI, which is based on the branch support analyses of the independent data sets, and where the reliability of the nodes is assessed using three measures: the supertree Bootstrap percentage and two other values calculated from the separate analyses: the mean branch support (mean Bootstrap percentage or mean posterior probability) and the reproducibility index.', 'In contrast to other similar software, the program FreeTree (available at http://www.natur.cuni.cz/~flegr/programs/freetree or http://ijs.sgmjournals.org/content/vol51/issue3/) can also assess the robustness of the tree topology by bootstrap, jackknife or operational taxonomic unit-jackknife analysis.', 'Unlike any previous tool for inferring phylogenies from rearrangement data, TIBA uses novel methods of robustness estimation to provide support values for the edges in the inferred tree.', 'Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator.', 'Moreover, whereas phylogenetic analyses from sequence data are deemed incomplete unless bootstrapping scores (a measure of confidence) are given for each tree edge, no equivalent to bootstrapping exists for rearrangement-based phylogenetic analysis.', 'We also describe a novel approach to estimate the robustness of results-an equivalent to the bootstrapping analysis used in sequence-based phylogenetic reconstruction.', 'The standard deviation also suggests the reliability level of the branch order.', 'Assessment of the reliability of a given phylogenetic hypothesis is an important step in phylogenetic analysis.', 'The reliability of the phylogenetic trees was probed with the bootstrapping of 100 replicates of the original sequence alignments.']
['The methods for assessing the robustness/reliability of the topology of the inferred phylogenetic trees are: the widely used bootstrap method and the jackknife method.', 'In contrast to other similar software, the program FreeTree (available at http://www.natur.cuni.cz/~flegr/programs/freetree or http://ijs.sgmjournals.org/content/vol51/issue3/) can also assess the robustness of the tree topology by bootstrap, jackknife or operational taxonomic unit-jackknife analysis. (PMID: 11411692)']
['bootstrap', 'jackknife']