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--- phylogeny_with_beast [2013/07/01 18:22]
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 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 63: / Line 64: @@
 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|}}
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 **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|}}