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--- buildingaphylogeny [2013/07/01 20:19]
anniearchambault
+++ buildingaphylogeny [2013/09/16 08:33] (current)
anniearchambault
@@ Line 2: / Line 2: @@
 A QCBS workshop given by Annie Archambault, to the QCBS students and researchers
-Sign up before June 18, 2013 [[http://qcbs.ca/training/workshops/phylogenetics-workshop/|on this page of the QCBS website]].
+Sign up [[http://qcbs.ca/training/workshops/phylogenetics-workshop/|on this page of the QCBS website]].
 ===About the workshop===
   * The target audience is researchers and students who will have to build a phylogenetic tree for their coming projects, but who don't quite know which program or which parameter to use.
-  * The workshop will be held Tuesday, July 2 (12:30 PM to 4:00 PM) and Wednesday July 3 (9:30 AM to 12:30 AM)
+  * The workshop will be held Monday September 16, 2013, 1:00 PM to 4:PM. The second day, September 17, 9:30 AM to 12:30 PM.
-  * The computer room is located in the Stewart Biology Building (4th floor, room N4-17)
+  * The computer room is located in Université Laval, Local 3434-E, Pavillon Paul Comtois
-  * The slides and presentation will be in English, but Annie also speaks French, and questions in French will be welcome and answered in French.
+  * The slides are in English, but presentation will be in French.
   * No food or drink is allowed in the computer room.
@@ Line 15: / Line 15: @@
   * Students from UdeM, UQAM and Concordia will be able to connect to the internet through Eduroam, with their usual home university connection.
   * If you plan on using your own computer, simply download the following programs
-    * SuiteMSA http://bioinfolab.unl.edu/~canderson/SuiteMSA/ ; or BioEdit [[http://www.mbio.ncsu.edu/BioEdit/bioedit.html|BioEdit]]
+    * [[http://www.jalview.org/|JalView]] with the [[http://www.jalview.org/webstart/jalview.jnlp|Launch JalViewD Desktop]] that uses Java Web Start; or [[http://www.mbio.ncsu.edu/BioEdit/bioedit.html|BioEdit]]; or SuiteMSA http://bioinfolab.unl.edu/~canderson/SuiteMSA/
     * JModelTest2 https://code.google.com/p/jmodeltest2/
     * ClustalX http://www.clustal.org/download/current/
@@ Line 33: / Line 33: @@
 I have been able to install the following programs on a Mac OS X 10.6.8 (64 bit). I have not tried any other operating system. You will find here the exact commands I used, but every user is welcome to modify them according to their operating system.
-**SuiteMSA**
+**JalView**
-Anderson, C.L., C.L. Strope, and E.N. Moriyama. 2011. [[http://www.biomedcentral.com/1471-2105/12/184/abstract|SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation]]. BMC Bioinformatics 12: 184.\\
+Waterhouse, A.M., et al. 2009. [[http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btp033|Jalview Version 2 - a multiple sequence alignment editor and analysis workbench]]. Bioinformatics 25: 1189–1191. \\
 This program will here simply be used to look at a sequence alignment created by other command line programs. \\
-Download the program at http://bioinfolab.unl.edu/~canderson/SuiteMSA/ \\
+Click on the "Launch Jalview Desktop" top right corner, and click "Open with Java Web Start". Allow the application to access your computer. \\
-Open the .jar file, located here: SuiteMSA_Package1.3.22B/SuiteMSA-1.3.22B/SuiteMSA-1.3.22B.jar \\
+Close the example windows shown. Click File/Input alignment/From file.
-If you are having problems with SuiteMSA, [[http://www.jalview.org/|JalView]] is also a good viewer for sequence alignment. I realized that SuiteMSA does not run on Windows, [[http://www.mbio.ncsu.edu/BioEdit/bioedit.html|BioEdit]] is a good option for that OS.
 **ClustalX**
@@ Line 48: / Line 47: @@
 **PRANK**
-Löytynoja, A., and N. Goldman. 2010. [[http://www.biomedcentral.com/1471-2105/11/579/abstract|webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser]]. BMC Bioinformatics 11: 579.
+Löytynoja, A., and N. Goldman. 2010. [[http://www.biomedcentral.com/1471-2105/11/579/abstract|webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser]]. BMC Bioinformatics 11: 579.  \\
+Löytynoja, A., and N. Goldman. 2005. [[http://www.pnas.org/content/102/30/10557|An algorithm for progressive multiple alignment of sequences with insertions]]. Proceedings of the National Academy of Sciences of the United States of America 102: 10557–10562 \\
 Dowload the program http://code.google.com/p/prank-msa/downloads/list. The README is here http://code.google.com/p/prank-msa/wiki/PRANK?tm=6 \\
 In the terminal, change directory to where the compressed file is located. Uncompress by typing: \\
@@ Line 58: / Line 58: @@
 I had success by typing: \\
 sudo ./prank -d=/Users/anniearchambault/Documents/learning_teaching/Alignment_and_phylogeny_building/Protea_Faurea_ITS_trnL_75seq.fasta \\
-The output file will be named output.best.fas . Open it in any sequence viewer. My favorite one is [[www.genious.com|Geneious]], but it is commercial. The SuiteMSA is free.
+For the Fungal_ITS_ref_sequence_nl.fasta_.txt, rename sequences with shorter names by typing this command: \\
+cut  -f 1-3 -d ' ' Fungal_ITS_ref_sequence_nl.fasta_.txt > Fungal_ITS_ref_sequence_nl_trim.fasta
+The output file will be named output.best.fas . Open it in any sequence viewer. My favorite one is [[http://www.genious.com|Geneious]], but it is commercial. JalView is free.
 in Windows, type: \\
@@ Line 105: / Line 108: @@
 sudo make install \\
 fsa /Users/anniearchambault/Documents/learning_teaching/Alignment_and_phylogeny_building/Protea_Faurea_ITS_trnL_75seq.fasta >/Users/anniearchambault/Documents/learning_teaching/Alignment_and_phylogeny_building/Protea_Faurea_ITS_trnL_75seq.mfa \\
+or, for numerous sequences:  \\
+fsa /Users/anniearchambault/Documents/learning_teaching/Alignment_and_phylogeny_building/Protea_Faurea_ITS_trnL_75seq.fasta >/Users/anniearchambault/Documents/learning_teaching/Alignment_and_phylogeny_building/Protea_Faurea_ITS_trnL_75seq.mfa --fast \\
 Only for this program, I have been unable to complete the installation, and I have used instead the webserver http://orangutan.math.berkeley.edu/fsa/ \\
@@ Line 190: / Line 194: @@
 http://qcbs.ca/wp-content/uploads/2013/06/PR10_Fabaceae_11seqs.txt \\
 http://qcbs.ca/wp-content/uploads/2013/06/Oxytropis_ITSsequences_84seq.txt \\
-http://qcbs.ca/wp-content/uploads/2013/06/Fungal_ITS_ref_301_sequence.txt
+http://qcbs.ca/wp-content/uploads/2013/09/Fungal_ITS_ref_sequence_nl.fasta_.txt
+++++ Files of already aligned sequences - for cheaters!  |
+http://qcbs.ca/wp-content/uploads/2013/09/Oxytropis_ITS_prank_output.best_.fas_.txt \\
+http://qcbs.ca/wp-content/uploads/2013/09/Oxytropis_ITS_muscleout.afa_.txt \\
+http://qcbs.ca/wp-content/uploads/2013/09/PR10_Fabaceae_muscleout.afa_.txt \\
+http://qcbs.ca/wp-content/uploads/2013/09/PR10_Fabaceae_fsa.mfa_.txt \\
+http://qcbs.ca/wp-content/uploads/2013/09/PR10_Fabaceae_Prank_output.best_.fas_.txt \\
+http://qcbs.ca/wp-content/uploads/2013/09/PR10_Fabaceae_sate_test.marker001.PR10_Fabaceae_11seqs.aln_.txt \\
+http://qcbs.ca/wp-content/uploads/2013/09/PR10_Fabaceae_clustal.fasta_.txt \\
+http://qcbs.ca/wp-content/uploads/2013/09/Fungal_ITS_ref_sequence_nlMuscleout.afa_.txt \\
+http://qcbs.ca/wp-content/uploads/2013/09/SATE_test.marker001.Fungal_ITS_ref_sequence_nl.aln_.txt \\
+++++