Exact(1)
A phylogenetic tree based on all the individuals analyzed was constructed using maximum-likelihood (ML) and Bayesian Inference (BI) methods.
Similar(59)
Given the very high number of sequences analyzed, the phylogenetic tree was constructed using the Neighbor-joining method using PAUP* v 4.0 [45], with 1000 bootstraps for measuring branch robustness.
Average structural parameters of each fraction were analyzed and model molecular structure was constructed using improved B-L method.
Once experimental data were collected and analyzed, a bottom-up model was constructed using mathematical and computational methods to accurately portray the data and the ensuing dynamics.
The database was constructed using the dbase IV program and analyzed using R statistical software [ 18].
All the data were analyzed and graphs were constructed using Microsoft Excel software.
The data were analyzed and the graphs were constructed using the GraphPad Prism software (GraphPad, San Diego, CA, USA).
However, the networks analyzed in the literature have been constructed using very different time windows - a day [6], a week [7], one month [8], and several months (e.g. [9, 10]) - and therefore it is crucial to understand what features of the underlying system are captured by different aggregation intervals.
Nucleotide sequences were analyzed using SeqMan and alignments were constructed using Clustal X, both from the Lasergene software package (DNASTAR, Inc., Madison, WI).
Gene interaction networks were constructed using the Analyze Networks algorithm with default settings.
Genes containing DMRs were analyzed for GO and KEGG pathways enrichment and gene networks were constructed using IPA software.
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