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--- tutorials:eccb_t2_codeml [2012/09/07 14:37]
romainstuder
+++ tutorials:eccb_t2_codeml [2012/09/09 09:47] (current)
romainstuder
@@ Line 1: / Line 1: @@
 ==== 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 ===
@@ Line 65: / Line 108: @@
   - 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|}}
+The tree looks like:
+{{:tutorials:tree.png|}}
 == Execute CodeML ==
@@ Line 70: / Line 116: @@
 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>
@@ Line 148: / Line 196: @@
 codeml ./TF105351.Eut.3.53876.ctl
 codeml ./TF105351.Eut.3.53876.fixed.ctl
-<./code>
+</code>
 In Windows:
@@ Line 156: / Line 204: @@
 </code>
-It can take time, so 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.fixed.mlc.zip|TF105351.Eut.3.53876.fixed.mlc (null model)}}
@@ Line 163: / Line 213: @@
 == Step 1) Assign significance of the detection of positive selection on the selected branch: ==
-Two output files are produced:
-  * TF105351.Eut.3.53876.mlc (alternative model):
-  * TF105351.Eut.3.53876.fixed.mlc (null model):
 We retieve the likelihood values lnL1 and lnL0 from TF105351.Eut.3.53876.mlc and TF105351.Eut.3.53876.fixed.mlc files, respectively.
 We retieve the number of parameters np1 and np0 from TF105351.Eut.3.53876.mlc and TF105351.Eut.3.53876.fixed.mlc files, respectively.
@@ Line 173: / Line 221: @@
    * lnL(ntime: 41  np: 45):  **-4710.222252**      +0.000000  (lnL0)
-We can construct the LRT (you can use your favourise spreadsheet for that. Or even better: R):
+We can construct the LRT (you can use your favourite spreadsheet for that. Or even better with R):
 ΔLRT = 2×(lnL1 - lnL0) = 2×(-4707.210163 - (-4710.222252)) = 6.024178
@@ Line 179: / Line 227: @@
 The degree of freedom is 1 (np1 - np0 = 46 - 45).
-p-value = 0.014104 (under χ²) => significant.
+(With OpenOffice: 1-CHISQDIST(6.024178;1))
+p-value = 0.014104 (under χ²) => __significant!__
 A significant result with the branch-site codon model means that positive selection affected a subset of sites during a specific evolutionary time (also called episodic model of protein evolution).
@@ Line 195: / Line 245: @@
    * Position 36 has  a high probability (97.1%) of being under positive selection. It shifted from a lysine to a glycine.
    * Position 159 has a very high probability (99.3%) of being under positive selection.
+You can visualise the multiple in Jalview.
+- Open Jalview
+- 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.
 {{: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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