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phylogeny_with_beast [2013/07/01 21:16] anniearchambault |
phylogeny_with_beast [2013/09/11 13:06] anniearchambault |
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- | ====Testing evolutionary hypothesis with BEAST2.0==== | + | ====Dating a node with BEAST2.0==== |
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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**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|}} | ||