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Bootstrap test was performed with 1000 replicates to calculate the confidence of the different nodes.
The NJ analysis with the bootstrap test was performed in MEGA 4.0 [55] using pairwise deletion for gaps/missing data.
Bootstrap test was performed with 1,000 replicates.
In all cases bootstrap test was performed on 500 replicates.
The nonparametric bootstrap test was performed for 100 replicates.
The bootstrap test was performed with 1000 replications, and only the bootstraps values higher than 80% are displayed as black dots on the nodes.
A bootstrap test was performed to test if the difference in proportions of neighbouring loci in contigs and scaffolds were likely to occur as a consequence of random sampling error.
Bootstrap tests were performed with 100 replications in the MP and ML analyses.
Therefore, for the dimensional measures, non-parametric bootstrap tests were performed using the GLM model in Stata.
Bootstrap testing was performed for 500 repetitions.
Therefore, parametric bootstrap testing was performed specifying a topology reflecting the 'glob2/3 duplication-in Sophophora subgenus' scenario as alternative hypothesis H1 and a topology reflecting the ' glob2 or 3 deletion-in Drosophila subgenus' as null hypothesis (H0).
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