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--- phylogeny_with_beast [2013/07/01 18:22]
anniearchambault
+++ phylogeny_with_beast [2013/09/11 13:30] (current)
anniearchambault
@@ Line 1: / Line 1: @@
-====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 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 13: / Line 14: @@
 http://qcbs.ca/wp-content/uploads/2013/06/ProteaFaurea_trnL.txt
-The files include sequences of the ITS and the trnL regions, from 74 species of the //Protea// genus, which comprises a total of 115 species, and the same loci from one specimen of //Faurea//, the sister genus of //Protea//. According to another study, the split leading to  //Faurea// and to //Protea// is 28.4 Ma (central 95% range 24.4–32.3 Ma). With an approximate date for this single root node, and the DNA sequences in hand, we will try to answer the question: How old is one of the oldest clade in //Protea//, comprising //P. cryophila, P. lorea, P. pruinosa, P. scabriuscula, P. scolopendrifolia// ?
+The files include sequences of the ITS and the trnL regions, from 74 species of the //Protea// genus, which comprises a total of 115 species, and the same loci from one specimen of //Faurea//, the sister genus of //Protea//. According to another study, the split leading to  //Faurea// and to //Protea// is 28.4 Ma (central 95% range 24.4–32.3 Ma). With an approximate date for this single root node, and the DNA sequences in hand, we will try to answer the question: How old is one of the oldest clade in //Protea//, comprising //P. cryophila, P. pruinosa, P. scabriuscula, P. scolopendrifolia// ?
@@ 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 45: / Line 47: @@
 **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)
@@ Line 63: / Line 65: @@
 For the two created sets, check the monophyletic box, select Normal, Mean=28.4, Sigma=2.5, do not check the estimate box.
-Create two new taxon sets, for the trnL and the ITS tree, each containing the five species //P. cryophila, P. lorea, P. pruinosa, P. scabriuscula, P. scolopendrifolia//. Label the sets OldClade_ITS and OldClade_trnL. For each set, Select Normal, check the monophyletic box, and add a reasonable number for Mean, Mean=11, check the estimate box, Sigma=1, check estimate. \\
+Create two new taxon sets, for the trnL and the ITS tree, each containing the four species //P. cryophila, P. pruinosa, P. scabriuscula, P. scolopendrifolia//. Label the sets OldClade_ITS and OldClade_trnL. For each set, Select Normal, check the monophyletic box, and add a reasonable number for Mean, Mean=11, check the estimate box, Sigma=1, check estimate. \\
 {{:beast_taxaset_normal_1.png?400|}}
@@ 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|}}