Additionally, we also plan to implement other codon substitution models such as EMC (currently implemented in Selecton), which takes into account both mechanistic and empirical data and arguably better fits real sequence data [ 67].
The association between phylogeny and geography was statistically assessed in a Bayesian framework implemented in the BaTS program [23], which takes into account the phylogenetic uncertainty in the analysis.
The homogenization method is implemented using the graded finite element concept, which takes into account the continuous gradation inside the finite elements.
We then used gene set enrichment analysis as implemented in the GSEA tool [ 37] (which takes into account the entire distribution of log2ratios) to increase the power of the comparison of the results of all three platforms [ 36].
All samples were normalized using the TMM protocol implemented using the edgeR package in R [ 69], which takes into account differences in overall RNA populations across biological samples.
We used the STATA 9.0 software and the procedure "sttocc," which takes into account survival times, to implement this step.
The developed method implements a complete and irreducible geometric model for serial manipulator, which takes into account different sources of errors (link lengths, joint offsets, etc).
The decision on whether to implement the heat rule is made on the basis of the "wet bulb globe temperature", which takes into account temperature and other comfort factors, such as humidity and wind.
Moreover, the policy regarding IFs was implemented by the SRPBS, which took into consideration the preliminary results of this study.
We recognise that this is not the most accurate or reliable method for determining orthology, so we are working to implement tools such as Ortholuge [ 50] and GreenPhyl [ 51], which take into account phylogenetic information in addition to sequence similarity.
