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Bootstrap proportions were obtained after 100 pseudo-replicates generated with SeqBoot [34].
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Bootstrap CAT proportions were obtained after 5000 cycles with a conservative burnin of 1000 on 100 pseudo-replicates generated with Seqboot (Phylip package [ 53]).
Similar proportions are obtained for CLM states.
The 95% CI for each estimated proportion was obtained by using the bootstrap resampling method with 1,000 resamples.
Bootstrap proportions (BPs) were obtained after 1000 replicates by using 10 replicates of random stepwise additions of taxa.
95 per cent confidence intervals of cumulative proportion was obtained by bias corrected bootstrapping (5000 replications)[ 18].
ML bootstrap proportions were inferred using 1000 replicates.
Bootstrap proportions were calculated by analysis of 1500 replicates.
In order to estimate robustness, bootstrap proportions were computed after 1000 replications.
Bootstrap proportions were drawn on the tree with highest likelihood score from the 10 independent searches.
Bootstrap values were obtained from 1000 replicate samples using the proportion of invariable sites and gamma distribution parameters defined by PHYML.
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