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This procedure was assessed in the evidence dataset shown in the next section.
The complete evidence dataset and corresponding published evidence can be found in the additional file 1.
Maximum leaf stability based on bootstrapping is illustrated for the parsimony analysis of morphology, the combined molecular dataset, and the total evidence dataset.
In all other cases, except for the total evidence dataset, the use of the suboptimal strict clock resulted in lower rate estimates and higher ingroup ages.
We analyzed each of the eight DNA regions individually and the combined total evidence dataset, allowing the investigation of how rates of molecular evolution vary among DNA regions.
Preliminary ML analyses were conducted on all single gene fragments, and partitioned and unpartitioned concatenated sets for a total evidence dataset [ 96].
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Annotated genes and gene models from the MSU Rice Genome Annotation Project (Ouyang et al. 2007) were transferred from the previous MSU pseudomolecule build to the Os-Nipponbare-Reference-IRGSP-1.0 pseudomolecules and functional annotation updated to reflect new evidence datasets.
The predictions were run three times using different input evidence datasets: 1) the 9,613 high-confidence Trinity assembled transcripts (see above), 2) all Trinity assembled transcripts, and 3) no assembled transcripts.
Given the fact that 83% of the pseudogenes identified are in the unsupported category as defined by lack of EST and full-length cDNA support (Table 1), we investigated deeper expression evidence datasets provided by MPSS expression profiles.
The What Works centres are relatively cheap: compared with carrying out primary research (or commissioning consultants) as much of their work is based on making better use of existing evidence, including datasets that have already been collected.
Moreover, context boundaries (species, tissues, cell types, experiment types, disease) are set for the provenance of the pieces of evidence and datasets used for network building.
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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