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The major steps of the CPF approach with bootstrap sampling are summarized by the following pseudocode.
RAxML nuclear gene trees were then used for phylogenomic analyses of all targeted loci with complete taxon sampling (n = 761) using the MP-EST species tree approach with bootstrap evaluation of clade support implemented through the STRAW webserver (Shaw et al., 2013).
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We confirmed this tree using several independent approaches, with bootstrap support and clade credibility marked.
In addition, the original tree from this data set was generated and confirmed using several independent approaches, with bootstrap support and clade credibility marked [ 11] which snpTree cannot repeat as using bootstrapping is time-consuming.
Because measurement errors which affect observations on the efficiency frontier can create complicated patterns of serial correlation for observations that lie within that portion of the frontier, they proposed a truncated regression approach with a bootstrap procedure instead.
Congruence between morphological and molecular species limits was 97.8% when using a clustering approach with high bootstrap support and enforcing a monophyly requirement in the molecular results, while clustering and identification success was 99% using clustering with a relaxed bootstrap criterion.
We constructed the accessions' phylogenetic tree using a Neighbor-Joining approach with 100 bootstraps.
The q-value was calculated for each probe set using Storey's false discovery rate (FDR) approach with the bootstrapping method (Storey et al., 2004).
As a result, it will be necessary to approach this with bootstrapping analysis.
Relationships were calculated applying a NJ-approach with 1,000 bootstrap replicates based on Nei's distances in the R package poppr41,42.
To enable comparison of traditional parametric and nonparametric statistical approaches with nonparametric bootstrap statistics, we report the results of all tests in Tables S1, S2, S3.
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