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A total of 180 mixed one-day-old broiler chicks (Ross 308) were purchased from a local hatchery, weighed on arrival and randomly allocated to 18 pens (1 × 1 m) of 10 birds each, with equal numbers of male and females (tree replicates per each treatment) in a ventilated broiler house containing wood shavings as litter material.
Calculated Gelman-Rubin statistics for all parameters were below 1.20, indicating satisfactory convergence between tree replicates.
The split networks inferred from the housekeeping gene sequences and T3SS sequences each indicate three pairs of strains having a high frequency of supporting splits in the embedded quartets of the bootstrap tree replicates.
With 60% jackknife resampling, we could generate unbiased tree replicates for the next step of classification training and testing.
To minimize data dependence on the prediction model, 10 tree replicates were prepared through jackknife procedure, five from each dataset (see "Material & Methods").
4) Compute a consensus tree and corresponding confidence values on all internal branches by using the CONSENSE program in PHYLIP [ 23] from 50 tree replicates.
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The statistical unit was the tree with generally one tree replicate per origin and soil compartment.
2) Reconstructing a tree replicate from these genomes with new ortholog subsets.
Our specific comparison involved taking each of the 100 bootstrap replicates produced by a particular method and comparing every tree replicate with each of the sets of 100 bootstrap trees that had been constructed for all of the methods.
PHYML, using the same settings as described above, was first used to infer 100 ML bootstrap trees from each individual gene dataset, then the initial MP-EST species tree inference was repeated 100 times from each of the 248 individual bootstrap gene-tree replicates.
Many pictures in the book – of families cutting cane, of men shinning up coconut trees – replicate the rural sights I see when I visit.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com