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phylogeny_with_beast [2013/09/11 13:06]
anniearchambault
phylogeny_with_beast [2013/09/11 13:30]
anniearchambault
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 {{:​beast_subs_model1.png?​400|Substitution models in BEAUti for ITS}} {{:​beast_subs_model1.png?​400|Substitution models in BEAUti for ITS}}
  
-For the trnL, we will choose the model selected by JModelTest2 ​(look at the printed page) \\ +For the trnL, we will choose the model selected by JModelTest2 \\  
 +{{:​jmodeltest_seeresults.png?​200|best substitution models from jModelTest for trnL}}
 {{:​beast_subs_model_trnl.png?​400|Substitution models in BEAUti for trnL}} {{:​beast_subs_model_trnl.png?​400|Substitution models in BEAUti for trnL}}
  
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 **5** Setting the Priors \\  ​ **5** Setting the Priors \\  ​
-This step is the most complicated of the whole process. ​+This step is the **most critical and most complicated** of the whole process. ​
 For the Tree prior, we will select the Yule model. Yule models are generally appropriate with sequences from different species, while Coalescent models are for different populations of a same species. Do the same for both partitions (ITS and trnL) For the Tree prior, we will select the Yule model. Yule models are generally appropriate with sequences from different species, while Coalescent models are for different populations of a same species. Do the same for both partitions (ITS and trnL)