P. Librado, F.G. Vieira and J. Rozas
Universitat de Barcelona
Current Release: Version 1.35 (Nov 02, 2011)

BadiRate is a software package to estimate, within a phylogenetic context and by likelihood-based methods (or parsimony):

1. the gain, birth, death and innovation family turnover rates
   
2. most likely number of family members in internal nodes
   
3. families with turnover rates higher or lower than that estimated for the whole data

Downloads

• BadiRate Complete package (source code, documentation and data file examples)

• BadiRate Documentation (PDF) and VBadiRate examples (input/output data files in zip file) 

• BadiRate GitHub site

References

• Librado P, Vieira FG, and Rozas J., 2012. BadiRate: Estimating Family Turnover Rates by Likelihood-Based Methods. Bioinformatics 28:279-281.

• Librado, P., Rozas, J. 2022. Reconstructing gene gains and losses with BadiRate. Pp. 2134-232. In Luo, H. (ed.). Environmental Microbial Evolution: Methods and Protocols; Methods in Molecular Biology Series Vol. 2569. Humana Press, NJ, USA.

Bug Reports

Please send your questions, comments and bug reports emailing to pablo.librado_AT_ibe.upf-csic.es.