Input files for the analysis were generated with Beauti v1.5.4 using a partitioned alignment file of 80 individuals.
The data were cleaned (purged of inconsistent and/or nonsense values), organized, and merged to create files for the analysis.
Our results suggest that by using the original MPS files for the analysis of differential splicing, the false negative rate is unnecessarily increased.
Affymetrix provides these annotation files for the analysis of differential gene expression and reports that probe sets less suitable for this purpose were left out.
The data (File S3) and R code (File S2) for the analysis are provided.
We used the D. yakuba mask file for this analysis so that the results are directly comparable to the results among species and conservative as we likely mask more genes than necessary.
Both analyses were performed using the software PHYCAS [ 51], and the input file for this analysis is provided as Additional File 11.
PCR amplification was performed with the primers listed in File S1 for the analysis of cgRNA expression.
Figure 1 shows examples of the association between the genes' tendency of clustering and their PI (see Additional file 2 for the analysis of all bacteria).
The mapping file built for the analysis of data obtained with the Affymetrix GeneChip was validated on a dataset of genes differentially expressed during berry ripening, reported in [ 21].
To obtain sufficient file sizes for the analysis of time trends involving consultations, we opted to combine study data covering several years to maximize the statistical power for the cost estimation.
