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--- tutorials:eccb_t2_codeml [2012/09/09 07:55] – 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 163: / 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)}}

CATH