We used CAFE to model gene family size evolution across the phylogeny of leaf-cutting ants. We only included Acromyrmex species and Atta colombica in the analysis as these genomes were sequenced using the same approach (long-range Illumina libraries).
- Combine the MCL clustered gene families with the MCMCtree computed ultrametric tree
run.geneFamilies.mcl.sh - First run error estimation for each genome
run.CAFError.sh - Then run CAFE with 2 lambda/mu parameters on each species
run.CAFE.sh - Cluster these 2-parameter models to find models that can converge.
analyseCAFEmodels.Rmd - Run LRT tests to compare models
CAFE.lhtest.R - Analyse final CAFE output
analyseCAFEoutput.Rmd