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tutorials:eccb_t2_codeml [2012/09/07 15:22]
romainstuder 		tutorials:eccb_t2_codeml [2012/09/09 09:47] (current)
romainstuder
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 ==== CodeML/PAML ==== ==== CodeML/PAML ====
 +
 +
 +=== Install of PAML ===
 +
 +Download it from here: http://abacus.gene.ucl.ac.uk/software/paml.html#download
 +
 +Windows (The bin/ folder already contains windows executables):
 +<code>
 +cd paml4.6/
 +</code>
 +
 +
 +Linux:
 +<code>
 +cd paml4.5/
 +rm bin/*.exe
 +cd src
 +make -f Makefile
 +ls -l
 +rm *.o
 +mv baseml basemlg codeml pamp evolver yn00 chi2 ../bin
 +chmod +x ../bin/*
 +</code>
 +
 +MacOSX:
 +<code>
 +cd paml4.6/
 +rm bin/*.exe
 +cd src
 +cc -O2 -o baseml baseml.c tools.c -lm
 +cc -O2 -o basemlg basemlg.c tools.c -lm
 +cc -O2 -o codeml codeml.c tools.c -lm
 +cc -O2 -o pamp pamp.c tools.c -lm
 +cc -O2 -o mcmctree mcmctree.c tools.c -lm
 +cc -O2 -o evolver evolver.c tools.c -lm
 +cc -O2 -o yn00 yn00.c tools.c -lm
 +cc -O2 -o chi2 chi2.c -lm
 +ls -l
 +rm *.o
 +mv baseml basemlg codeml pamp evolver yn00 chi2 ../bin
 +chmod +x ../bin/*
 +</code>
 +
  
 === Theoretical principles of the Branch-site model === === Theoretical principles of the Branch-site model ===
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   - A command file where all parameters to run CodeML under the alternative model are specified: {{:tutorials:tf105351.eut.3.53876.ctl.zip|}}   - A command file where all parameters to run CodeML under the alternative model are specified: {{:tutorials:tf105351.eut.3.53876.ctl.zip|}}
   - A command file where all parameters to run CodeML under the null model are specified: {{:tutorials:tf105351.eut.3.53876.fixed.ctl.zip|}}   - A command file where all parameters to run CodeML under the null model are specified: {{:tutorials:tf105351.eut.3.53876.fixed.ctl.zip|}}
 +
 +The tree looks like:
 +{{:tutorials:tree.png|}}
  
 == Execute CodeML == == Execute CodeML ==
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 Run command file (alternative model): Run command file (alternative model):
  
-We estimate the Ts/Tv ratio (fix_kappa = 0) and the dN/dS (fix_omega = 0). The branch-site model is specified by setting the model parameter to 2 (different dN/dS for branches) and the NSsites value to 2 (which allows 3 categories for sites: purifying, neutral and positive selection).+We estimate the Ts/Tv ratio (fix_kappa = 0) and the dN/dS (fix_omega = 0). The branch-site model is specified by setting these two parameters: 
 +    * model = 2 (different dN/dS for branches)  
 +    * NSsites value to 2 (which allows 3 categories for sites: purifying, neutral and positive selection).
  
 <code> <code>
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 Two mlc output files are produced (as it can take time, you can download them directly in the next step).: Two mlc output files are produced (as it can take time, you can download them directly in the next step).:
   * {{:tutorials:tf105351.eut.3.53876.mlc.zip|TF105351.Eut.3.53876.mlc (alternative model)}}   * {{:tutorials:tf105351.eut.3.53876.mlc.zip|TF105351.Eut.3.53876.mlc (alternative model)}}
-  * {{:tutorials:tf105351.eut.3.53876.fixed.ctl.zip|TF105351.Eut.3.53876.fixed.mlc (null model)}} +  * {{:tutorials:tf105351.eut.3.53876.fixed.mlc.zip|TF105351.Eut.3.53876.fixed.mlc (null model)}}
  
  
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 - Open Jalview - Open Jalview
 +
 - Load TF105351.Eut.3.phy - Load TF105351.Eut.3.phy
 +
 - Then: Calculate->translate cDNA. (tips: by moving the pointer on the amino acids alignment, you can see the corresponding codon in the nucleotide alignment. - Then: Calculate->translate cDNA. (tips: by moving the pointer on the amino acids alignment, you can see the corresponding codon in the nucleotide alignment.
  
 {{:tutorials:tf105351.eut.3.aln.png|}} {{:tutorials:tf105351.eut.3.aln.png|}}
  
 +
 +
 +
 +
 +=== Using other models ===
 +
 +Other models can be tested by changing these parameters model and NSsites.
 +
 +== Example 1: ==
 +
 +Site model M1 (neutral):
 +    * model = 0 (dN/dS doesn't vary on branches) 
 +    * NSsites = 1 (which allows 2 categories for sites: purifying and neutral).
 +
 +Site model M2a (positive selection):
 +    * model = 0 (dN/dS doesn't vary on branches) 
 +    * NSsites = 2 (which allows 3 categories for sites: purifying, neutral and positive selection).
 +
 +Then we can compare M1 and M2a by the likelihood ratio test.
 +
 +
 +== Example 2: ==
 +
 +
 +Branch model M0:
 +    * model = 0 (dN/dS doesn't vary on branches) 
 +    * NSsites = 0 (dN/dS doesn't vary on sites).
 +
 +Branch model M2 with different dN/dS (positive selection on selected branches):
 +    * model = 2 (different dN/dS for branches) 
 +    * NSsites = 2 (dN/dS doesn't vary on sites).
 +
 +Then we can compare M0 and M2 by the likelihood ratio test.

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