Data from Oakley et al (2005) MBE
1. After grouping genes into gene families, I conducted phylogenetic analyses on each of the families. I ended up using Maximum Likelihood to estimate the gene trees used in the paper for further analysis. (I had also conducted Bayesian analyses, but those didn't make it to the final paper, I can dig up those analyses if anyone might be interested). The following file is "executable" by Paup to reproduce all the trees used for final data analyses. The file also therefore contains all of the aligned sequences.
2. I then analyzed evolution of gene expression using microarray data. The following is a table of the 10 gene families analyzed, with links to tree files (nexus format) and files that can be opened in Mesquite, which contain both trees and all microarray data. The likelihood of the models presented in the paper can be calculated using CoMET, which is implemented in Mesquite.
| Gene Family Name/Function | Tree File | Mesquite File* |
|---|---|---|
| Kinases | Tree file | Mesquite File |
| ADP Ribosylation | Tree file | Mesquite File |
| Alpha-Glucosidases | Tree file | Mesquite File |
| ABC Transporters | Tree file | Mesquite File |
| Heat Shock Proteins | Tree file | Mesquite File |
| GTP Binding | Tree file | Mesquite File |
| DUP (Unknown function) | Tree file | Mesquite File |
| Helicases | Tree file | Mesquite File |
| Permeases | Tree file | Mesquite File |
| Hexose transporters | Tree file | Mesquite File |
* Thanks to Adam Kinney for preparing most of the Mesquite Files