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phylogeny_with_beast [2013/07/09 12:54] anniearchambault |
phylogeny_with_beast [2013/09/11 13:30] (current) anniearchambault |
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| For details, read http://beast2.cs.auckland.ac.nz/index.php/Main_Page and http://beast2.cs.auckland.ac.nz/index.php/FAQ . | For details, read http://beast2.cs.auckland.ac.nz/index.php/Main_Page and http://beast2.cs.auckland.ac.nz/index.php/FAQ . | ||
| + | For any problem, do not hesitate to browse through the list of questions on the BEAST forum https://groups.google.com/forum/#!forum/beast-users . | ||
| ===Exercise description=== | ===Exercise description=== | ||
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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) | ||
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| **8** Run the analysis \\ | **8** Run the analysis \\ | ||
| Save your the BEAUti settings as a .xml file. Open the BEAST program, Load the .xml file, and run the search. When completed, modify the name. This is because for you be able to re-launch an BEAST analysis with the same .xml file. | Save your the BEAUti settings as a .xml file. Open the BEAST program, Load the .xml file, and run the search. When completed, modify the name. This is because for you be able to re-launch an BEAST analysis with the same .xml file. | ||
| + | ++++ Or use this example file | | ||
| + | Here is one xml file: http://qcbs.ca/wp-content/uploads/2013/09/ProteaFaurea_ITS_trnl_test18.xml_.txt | ||
| + | ++++ | ||
| **9** Analyze the results \\ | **9** Analyze the results \\ | ||
| Open the program Tracer. Load the newly created .log file. \\ | Open the program Tracer. Load the newly created .log file. \\ | ||
| Select the two mrcatime(OldClade) values, and look at the Estimates. \\ | Select the two mrcatime(OldClade) values, and look at the Estimates. \\ | ||
| - | Try answer the questions \\ | + | Try answer the questions http://qcbs.ca/wp-content/uploads/2013/09/Beast_questions3.pdf \\ |
| {{:tracer_mrca_old.png?400|}} | {{:tracer_mrca_old.png?400|}} | ||
