Added Branch specific and pairwise null and alternative control files.

Author: icwells

controlFiles/branchSpecific.ctl controlFiles/branchSpecificAlt.ctlcontrolFiles/branchSpecific.ctl renamed to controlFiles/branchSpecificAlt.ctl

@@ -0,0 +1,42 @@
+	  seqfile = sample.txt * sequence data filename
+     treefile = samplephy.phy     * tree structure file name
+      outfile = mlc           * main result file name
+	
+	   noisy = 0  * 0,1,2,3,9: how much rubbish on the screen
+      verbose = 0  * 0: concise; 1: detailed, 2: too much
+      runmode = 0  * 0: user tree;  1: semi-automatic;  2: automatic
+                   * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise
+
+      seqtype = 1  * 1:codons; 2:AAs; 3:codons-->AAs
+    CodonFreq = 0  * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
+        clock = 0  * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis
+       aaDist = 0  * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
+   aaRatefile = dat/jones.dat  * only used for aa seqs with model=empirical(_F)
+                   * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own
+        model = 0
+                   * models for codons:
+                       * 0:one, 1:b, 2:2 or more dN/dS ratios for branches
+
+      NSsites = 0  * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs;
+                   * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ
+                   * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1;
+                   * 13:3normal>0
+
+        icode = 0  * 0:universal code; 1:mammalian mt; 2-10:see below
+    fix_kappa = 0  * 1: kappa fixed, 0: kappa to be estimated
+        kappa = 3  * initial or fixed kappa
+    fix_omega = 1  * 1: omega or omega_1 fixed, 0: estimate 
+        omega = 1  * initial or fixed omega, for codons or codon-based AAs
+
+    fix_alpha = 1  * 0: estimate gamma shape parameter; 1: fix it at alpha
+        alpha = 0  * initial or fixed alpha, 0:infinity (constant rate)
+       Malpha = 0  * different alphas for genes
+        ncatG = 8  * # of categories in dG of NSsites models
+
+        getSE = 0  * 0: don't want them, 1: want S.E.s of estimates
+ RateAncestor = 0  * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
+
+   Small_Diff = .5e-6
+    cleandata = 1  * remove sites with ambiguity data (1:yes, 0:no)?
+       method = 1  * Optimization method 0: simultaneous; 1: one branch a time
+

controlFiles/branchSpecificNull.ctl

@@ -16,7 +16,7 @@
         model = 0  * models for codons:
                        * 0:one, 1:b, 2:2 or more dN/dS ratios for branches
 
-      NSsites = 0  * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs;
+      NSsites = 2  * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs;
                    * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ
                    * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1;
                    * 13:3normal>0

controlFiles/pairwise.ctl controlFiles/pairwiseAlt.ctlcontrolFiles/pairwise.ctl renamed to controlFiles/pairwiseAlt.ctl

@@ -0,0 +1,41 @@
+      seqfile = 
+     treefile =  
+      outfile = 
+	
+	    noisy = 0  * 0,1,2,3,9: how much rubbish on the screen
+      verbose = 0  * 0: concise; 1: detailed, 2: too much
+      runmode = -2  * 0: user tree;  1: semi-automatic;  2: automatic
+                   * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise
+
+      seqtype = 1  * 1:codons; 2:AAs; 3:codons-->AAs
+    CodonFreq = 0  * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
+        clock = 0  * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis
+       aaDist = 0  * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
+   aaRatefile = dat/jones.dat  * only used for aa seqs with model=empirical(_F)
+                   * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own
+        model = 0  * models for codons:
+                       * 0:one, 1:b, 2:2 or more dN/dS ratios for branches
+
+      NSsites = 1  * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs;
+                   * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ
+                   * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1;
+                   * 13:3normal>0
+
+        icode = 0  * 0:universal code; 1:mammalian mt; 2-10:see below
+    fix_kappa = 0  * 1: kappa fixed, 0: kappa to be estimated
+        kappa = 3  * initial or fixed kappa
+    fix_omega = 0  * 1: omega or omega_1 fixed, 0: estimate 
+        omega = 1 * initial or fixed omega, for codons or codon-based AAs
+
+    fix_alpha = 1  * 0: estimate gamma shape parameter; 1: fix it at alpha
+        alpha = 0 * initial or fixed alpha, 0:infinity (constant rate)
+       Malpha = 0  * different alphas for genes
+        ncatG = 8  * # of categories in dG of NSsites models
+
+        getSE = 0  * 0: don't want them, 1: want S.E.s of estimates
+ RateAncestor = 0  * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
+
+   Small_Diff = .5e-6
+    cleandata = 1  * remove sites with ambiguity data (1:yes, 0:no)?
+       method = 1  * Optimization method 0: simultaneous; 1: one branch a time
+