Citation

The citation for latest version of CAFE is:

Han, M. V., Thomas, G. W. C., Lugo-Martinez, J., and Hahn, M. W. Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3. Molecular Biology and Evolution 30, 8 (2013)

The citation for CAFE v2.0 is:

Hahn, M. W., Demuth, J. P., and Han, S. -G. Accelerated rate of gene gain and loss in primates. Genetics 177, (2007)

The citation for the original version of CAFE is:

De Bie, T., Cristianini, N., Demuth, J. P., and Hahn, M. W. CAFE: a computational tool for the study of gene family evolution. Bioinformatics 22, (2006)

Original development of the statistical framework and algorithms implemented in CAFE are published in:

Hahn, M. W., DeBie, T., Stajich, J. E., Nguyen, C., and Cristianini, N. Estimating the tempo and mode of gene family from comparative genomic data. Genomic Research 15, 8 (2005)