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Morphological features were compared using all available data.
Then, the analyzed data were compared using all of the subjects.
The slopes before and after study entry were globally compared using all data points in the mixed model.
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The complete proteomes were compared using all-against-all BLAST, and then clustered using OrthoMCL (24).
Initially, all protein sequences in Refseq were compared using an all-vs.-all blast search, and all significant matches were identified (E<1e-7).
To build ortholog clusters, all protein sequences from the 11 fungi were compared using an all-against-all BLAST (requiring 1e−5), then clustered with the OrthoMCL2 pipeline (Li et al. 2003) to identify ortholog groups using default parameters.
All pairs of 3D patterns identified in the two tested proteins are compared using an all-versus-all approach.
Treatments were then compared using the all-pairwise Tukey Kramer HSD procedure (JMP9).
When a significant F-ratio was obtained, means were compared using the all pairwise multiple comparison procedure of Holm-Sidak.
All metagenomic datasets were combined into a single FASTA file and compared using a complete all-verses-all NCBI BLAST [ 41].
Primary outcomes will be compared using logistic regression models using all available data and adjusted for baseline values.
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