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Note that the backbone phylogeny we built using the bootstrap-based extended majority rule was consistent with the species phylogeny inferred in [ 68].
Relatedness trees were constructed based on chord distances using the neighbor joining algorithm, and a majority rule bootstrap consensus tree was built using the programs NEIGHBOR and CONSENSE in PHYLIP v. 3.65 [64].
Phylogenetic trees were built using the neighbor-joining algorithm [ 40] and tested with 1000 rounds of bootstrapping.
For Figure 1 figure supplement 6, the maximum likelihood tree was built using the PhyML server (Dereeper et al., 2008) using default parameters and bootstraps set to 100.
Each of the classification trees is built using a bootstrap sample of the data, and at each split the candidate set of variables is comprised of a random subset.
Second, every tree is built using a bootstrap sample of the observations.
Secondly, every tree is built using a bootstrap sample of the observations.
This means that only in less than 50% of the trees built using bootstrap do we find separation of the protists cluster and the plant cluster.
Each tree is built using a bootstrap sample of objects.
When manual curation of taxa or alignments was required, additional trees were built using RAxML rapid bootstrapping (100 replications) and maximum-likelihood (ML) search assuming a WAG amino acid model of substitution and Γ site heterogeneity model (Stamatakis 2006).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com