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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.
In all cases bootstrap test was performed on 500 replicates.
The nonparametric bootstrap test was performed for 100 replicates.
Bootstrap test was performed with 1,000 replicates.
A bootstrap test was performed by randomly resampling 63.21% of the proteomes for each species 100 times, as described previously (Zuo et al. 2010).
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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).
Bootstrapping test was performed 1000 times, whereby branches with less than 80% bootstrap values have been dissolved.
The bootstrap tests were performed using the R environment package Pvclust [28].
Bootstrap tests were performed with 100 replications in the MP and ML analyses.
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