--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputs/for_paml/test.cnt	Sun Nov 09 10:56:06 2025 +0000
@@ -0,0 +1,36 @@
+      seqfile = test.codon
+     treefile = test.tree
+      outfile = test.codeml
+
+        noisy = 0   * 0,1,2,3,9: how much rubbish on the screen
+      verbose = 0   * 1: detailed output, 0: concise output
+      runmode = -2  * 0: user tree;  1: semi-automatic;  2: automatic
+                    * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise
+
+    cleandata = 1   * "I added on 07/07/2004" Mikita Suyama
+
+      seqtype = 1   * 1:codons; 2:AAs; 3:codons-->AAs
+    CodonFreq = 2   * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
+        model = 2
+                    * models for codons:
+                        * 0:one, 1:b, 2:2 or more dN/dS ratios for branches
+
+      NSsites = 0   * dN/dS among sites. 0:no variation, 1:neutral, 2:positive
+        icode = 0   * 0:standard genetic code; 1:mammalian mt; 2-10:see below
+        Mgene = 0   * 0:rates, 1:separate; 2:pi, 3:kappa, 4:all
+
+    fix_kappa = 0   * 1: kappa fixed, 0: kappa to be estimated
+        kappa = 2   * 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-transltd 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 = 4   * # of categories in the dG or AdG models of rates
+
+        clock = 0   * 0: no clock, unrooted tree, 1: clock, rooted tree
+        getSE = 0   * 0: don't want them, 1: want S.E.s of estimates
+ RateAncestor = 0   * (1/0): rates (alpha>0) or ancestral states (alpha=0)
+       method = 0   * 0: simultaneous; 1: one branch at a time
+