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--- phylogeny_with_beast [2013/07/09 12:54]
anniearchambault
+++ phylogeny_with_beast [2013/09/11 13:25]
anniearchambault
@@ Line 2: / Line 2: @@
 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===
@@ Line 37: / Line 38: @@
 {{: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}}
@@ Line 83: / Line 85: @@
 **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.
+++++ 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 \\
 Open the program Tracer. Load the newly created .log file.  \\
 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|}}