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BadiRate: Estimating Family Turnover Rates by Likelihood-Based Methods  

2014-04-05 22:13:22|  分类: 生物信息分析 |  标签: |举报 |字号 订阅

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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

BadiRate: Estimating Family Turnover Rates by Likelihood-Based Methods - 喜欢吃桃子 - wangyufeng的博客

 Fig. 1. Relative performance of the different methods. Computer simulations based on gene families of 5 members (S = 5) at the most internal node, and a null innovation rate (I = 0). (A) The boxplot represents the error values (see Supplementary Material) distribution across tested methods. (B and C) Surface plots showing the error values of the ML estimates in scenarios simulated under a combination biologically-realistic birth and death rates. Analysis under the BDI, LI and P models are conducted with BadiRate and are depicted in blue, green and cyan respectively. The model implemented in CAFE is depicted in red..Birth and death rates are measured in number of events per gene per million years (See the Supplementary Material for details).


Download

   BadiRate Complete package (source code, documentation and data file examples): 
   badirate-1.35.tar.gz    

  BadiRate Documentation formulari pdf    and BadiRate examples: input/output data files  examples.zip


References

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

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