add new PAML ctl files for tests

Tests/PAML/Control_files/baseml/nparK1.ctl

@@ -0,0 +1,36 @@
+      seqfile = PAML/alignment.phylip
+     treefile = PAML/species.tree
+
+      outfile = temp.out       * main result file
+        noisy = 0   * 0,1,2,3: how much rubbish on the screen
+      verbose = 0   * 1: detailed output, 0: concise output
+      runmode = 0   * 0: user tree;  1: semi-automatic;  2: automatic
+                    * 3: StepwiseAddition; (4,5):PerturbationNNI
+
+        model = 6   * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85
+                    * 5:T92, 6:TN93, 7:REV, 8:UNREST, 9:REVu; 10:UNRESTu
+
+        Mgene = 1   * 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff
+
+*        ndata = 100
+        clock = 0   * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis
+    fix_kappa = 0   * 0: estimate kappa; 1: fix kappa at value below
+        kappa = 5  * initial or fixed kappa
+
+    fix_alpha = 0   * 0: estimate alpha; 1: fix alpha at value below
+        alpha = 0.5   * initial or fixed alpha, 0:infinity (constant rate)
+       Malpha = 0   * 1: different alpha's for genes, 0: one alpha
+        ncatG = 5   * # of categories in the dG, AdG, or nparK models of rates
+       fix_rho = 1
+          rho = 0
+	nparK = 1   * rate-class models. 1:rK, 2:rK&fK, 3:rK&MK(1/K), 4:rK&MK
+
+        nhomo = 0   * 0 & 1: homogeneous, 2: kappa for branches, 3: N1, 4: N2
+        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
+
+   Small_Diff = 7e-6
+    cleandata = 1  * remove sites with ambiguity data (1:yes, 0:no)?
+*        icode = 0  * (with RateAncestor=1. try "GC" in data,model=4,Mgene=4)
+*  fix_blength = -1  * 0: ignore, -1: random, 1: initial, 2: fixed
+       method = 0  * Optimization method 0: simultaneous; 1: one branch a time

Tests/PAML/Control_files/baseml/nparK2.ctl

@@ -0,0 +1,36 @@
+      seqfile = PAML/alignment.phylip
+     treefile = PAML/species.tree
+
+      outfile = temp.out       * main result file
+        noisy = 0   * 0,1,2,3: how much rubbish on the screen
+      verbose = 0   * 1: detailed output, 0: concise output
+      runmode = 0   * 0: user tree;  1: semi-automatic;  2: automatic
+                    * 3: StepwiseAddition; (4,5):PerturbationNNI
+
+        model = 6   * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85
+                    * 5:T92, 6:TN93, 7:REV, 8:UNREST, 9:REVu; 10:UNRESTu
+
+        Mgene = 1   * 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff
+
+*        ndata = 100
+        clock = 0   * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis
+    fix_kappa = 0   * 0: estimate kappa; 1: fix kappa at value below
+        kappa = 5  * initial or fixed kappa
+
+    fix_alpha = 0   * 0: estimate alpha; 1: fix alpha at value below
+        alpha = 0.5   * initial or fixed alpha, 0:infinity (constant rate)
+       Malpha = 0   * 1: different alpha's for genes, 0: one alpha
+        ncatG = 5   * # of categories in the dG, AdG, or nparK models of rates
+       fix_rho = 1
+          rho = 0
+	nparK = 2   * rate-class models. 1:rK, 2:rK&fK, 3:rK&MK(1/K), 4:rK&MK
+
+        nhomo = 0   * 0 & 1: homogeneous, 2: kappa for branches, 3: N1, 4: N2
+        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
+
+   Small_Diff = 7e-6
+    cleandata = 1  * remove sites with ambiguity data (1:yes, 0:no)?
+*        icode = 0  * (with RateAncestor=1. try "GC" in data,model=4,Mgene=4)
+*  fix_blength = -1  * 0: ignore, -1: random, 1: initial, 2: fixed
+       method = 0  * Optimization method 0: simultaneous; 1: one branch a time

Tests/PAML/Control_files/baseml/nparK3.ctl

@@ -0,0 +1,36 @@
+      seqfile = PAML/alignment.phylip
+     treefile = PAML/species.tree
+
+      outfile = temp.out       * main result file
+        noisy = 0   * 0,1,2,3: how much rubbish on the screen
+      verbose = 0   * 1: detailed output, 0: concise output
+      runmode = 0   * 0: user tree;  1: semi-automatic;  2: automatic
+                    * 3: StepwiseAddition; (4,5):PerturbationNNI
+
+        model = 6   * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85
+                    * 5:T92, 6:TN93, 7:REV, 8:UNREST, 9:REVu; 10:UNRESTu
+
+        Mgene = 1   * 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff
+
+*        ndata = 100
+        clock = 0   * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis
+    fix_kappa = 0   * 0: estimate kappa; 1: fix kappa at value below
+        kappa = 5  * initial or fixed kappa
+
+    fix_alpha = 0   * 0: estimate alpha; 1: fix alpha at value below
+        alpha = 0.5   * initial or fixed alpha, 0:infinity (constant rate)
+       Malpha = 0   * 1: different alpha's for genes, 0: one alpha
+        ncatG = 5   * # of categories in the dG, AdG, or nparK models of rates
+       fix_rho = 1
+          rho = 0
+	nparK = 3   * rate-class models. 1:rK, 2:rK&fK, 3:rK&MK(1/K), 4:rK&MK
+
+        nhomo = 0   * 0 & 1: homogeneous, 2: kappa for branches, 3: N1, 4: N2
+        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
+
+   Small_Diff = 7e-6
+    cleandata = 1  * remove sites with ambiguity data (1:yes, 0:no)?
+*        icode = 0  * (with RateAncestor=1. try "GC" in data,model=4,Mgene=4)
+*  fix_blength = -1  * 0: ignore, -1: random, 1: initial, 2: fixed
+       method = 0  * Optimization method 0: simultaneous; 1: one branch a time

Tests/PAML/Control_files/baseml/nparK4.ctl

@@ -0,0 +1,36 @@
+      seqfile = PAML/alignment.phylip
+     treefile = PAML/species.tree
+
+      outfile = temp.out       * main result file
+        noisy = 0   * 0,1,2,3: how much rubbish on the screen
+      verbose = 0   * 1: detailed output, 0: concise output
+      runmode = 0   * 0: user tree;  1: semi-automatic;  2: automatic
+                    * 3: StepwiseAddition; (4,5):PerturbationNNI
+
+        model = 6   * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85
+                    * 5:T92, 6:TN93, 7:REV, 8:UNREST, 9:REVu; 10:UNRESTu
+
+        Mgene = 1   * 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff
+
+*        ndata = 100
+        clock = 0   * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis
+    fix_kappa = 0   * 0: estimate kappa; 1: fix kappa at value below
+        kappa = 5  * initial or fixed kappa
+
+    fix_alpha = 0   * 0: estimate alpha; 1: fix alpha at value below
+        alpha = 0.5   * initial or fixed alpha, 0:infinity (constant rate)
+       Malpha = 0   * 1: different alpha's for genes, 0: one alpha
+        ncatG = 5   * # of categories in the dG, AdG, or nparK models of rates
+       fix_rho = 1
+          rho = 0
+	nparK = 4   * rate-class models. 1:rK, 2:rK&fK, 3:rK&MK(1/K), 4:rK&MK
+
+        nhomo = 0   * 0 & 1: homogeneous, 2: kappa for branches, 3: N1, 4: N2
+        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
+
+   Small_Diff = 7e-6
+    cleandata = 1  * remove sites with ambiguity data (1:yes, 0:no)?
+*        icode = 0  * (with RateAncestor=1. try "GC" in data,model=4,Mgene=4)
+*  fix_blength = -1  * 0: ignore, -1: random, 1: initial, 2: fixed
+       method = 0  * Optimization method 0: simultaneous; 1: one branch a time