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The robustness of the MP tree was assessed by performing bootstrapping analysis with 1000 replicates, and gaps removed by complete deletion [21].
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The reliability of the branching order was estimated by performing bootstrap analysis (100 replicates).
The reliability of the phylogenetic trees was confirmed by performing bootstrap analysis.
Phylogenetic dendrograms were constructed by the neighbor-joining method and trees topology was evaluated by performing bootstrap analysis of 1000 data sets using MEGA 4.1 (Molecular Evolutionary Genetics Analysis) [ 31].
This was done by requesting AMOS to determine the significance level (p-value) of the indirect effects by performing bootstrapping in the modelling analysis [ 51].
In order to verify the topology of the Bayesian phylogenetic trees supported by the posterior probability, we performed bootstrap analysis using the Maximum Likelihood method implemented in RAxML software [ 72].
In addition, we performed bootstrap analysis with 100 replications.
Second, we analyze the spatial resolution of slip with respect to input data by performing a bootstrap analysis (with variable Vr), in which we randomly select 116 'new' data from the 116 input data, and reinvert.
Support for each branch was obtained by performing the bootstrap analysis with 100 replicates.
The tree topologies were evaluated by performing a bootstrap analysis with 1,000 replicates.
We estimated the variance of these measures by performing a bootstrap analysis (Efron 1979) over sets of functional maps grouped by experiment and subsequently estimating confidence intervals (CIs) for the measured distributions.
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