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2,000 bootstrap replicates were conducted for each of these four datasets.
To corroborate the Bayesian results [108], maximum likelihood analyses of the codon alignments and maximum parsimony and neighbour-joining analyses of the aa alignments with 1000 bootstrap replicates were conducted using PAUP 4.0b10 [109].
200 bootstrap replicates were conducted.
GTRCAT and GTRGAMMA options were used, 1000 rapid bootstrap replicates were conducted to assess bootstrap values.
One hundred and 1000 rapid bootstrap replicates were conducted for nuclear and plastid analyses, respectively.
In addition, maximum likelihood analysis with 1000 and maximum parsimony analysis with 1000 bootstrap replicates were conducted.
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A 1000 bootstrap replicates was conducted with the preferred model in PAUP* 4.0b10.
To test for this possibility, each taxon was successively removed from the dataset (N = 63 experiments) and subsequently a likelihood run (using RAxML) under the GTR + 3 model with 1000 rapid bootstrap replicates was conducted for each resulting dataset.
One thousand bootstrap resampling replicates were conducted to estimate support for the clades.
In both ML and MP bootstrapping, 1000 replicates were conducted.
Bootstrap analyses (100 replicates) were conducted as described above except the tree search initiated from a single parsimony tree per replicate.
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