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--- tutorials:eccb_t2_codeml [2012/09/07 15:43] – 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 73: / 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 161: / Line 206: @@
 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.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)}}
@@ Line 212: / Line 256: @@
 {{: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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