Reformatted commandlines for mcmctree doc.

Author: piyumalanthony

doc/Dating.md

@@ -8,8 +8,20 @@ icon: info-circle
 doctype: tutorial
 tags:
 - tutorial
-description: "Building time tree with node dates on phylogenetic trees."
+description: "Inferring time trees"
 sections:
+  - name: Bayesian dating with MCMCtree
+    url: bayesian-dating-with-mcmctree
+  - name: IQ2MC workflow for time tree inference
+    url: iq2mc-workflow-for-time-tree-inference
+  - name: Estimating the gradients and the Hessian for MCMCtree dating
+    url: estimating-the-gradients-and-the-hessian-for-mcmctree-dating
+  - name: Using partitions and Mixture models for approximate likelihood dating
+    url: partitions-and-mixture-models-for-approximate-likelihood-dating
+  - name: How to run MCMCtree
+    url: how-to-run-mcmctree
+  - name: Least Square Dating (LSD2)
+    url: least-square-dating
   - name: Inferring time tree with tip dates
     url: inferring-time-tree-with-tip-dates
   - name: Calibrating tree using ancestral dates
@@ -77,7 +89,10 @@ approximate likelihood dating.
 If the alignment file is called `example.phy` and the rooted tree file is called
 `example_tree.nwk`,
 
-    iqtree -s example.phy -m GTR+G4 -te example_tree.nwk --dating mcmctree --prefix example
+```
+iqtree -s example.phy -m GTR+G4 -te example_tree.nwk --dating mcmctree --prefix example
+```
+
 
 Note that, Here we generate the Hessian file for a fixed rooted tree. You can
 directly input the rooted tree which already contains fossil/tip calibration
@@ -102,7 +117,9 @@ input to MCMCtree to save compute.
 You can specify more parameters in the workflow to generate the control file
 accurately for the analysis with IQ-TREE.
 
-    iqtree -s example.phy -m GTR+G4 -te example_tree.nwk --dating mcmctree --mcmc-iter 20000,200,50000 --mcmc-bds 1,1,0.5 --mcmc-clock IND
+```
+iqtree -s example.phy -m GTR+G4 -te example_tree.nwk --dating mcmctree --mcmc-iter 20000,200,50000 --mcmc-bds 1,1,0.5 --mcmc-clock IND
+```
 
 * `--mcmc-iter burnin,samplefreq,nsample` : use to set number of burin samples,
 sample frequency and number of MCMC samples in the control file. In the above
@@ -117,7 +134,7 @@ Currently supported clocks models are EQUAL: global clock with equal rates, IND:
 independent rates model with independent rates across lineages and CORR:
 correlated clock model with auto-correlated rates across the lineages.
 
-Using partitions and Mixture models for approximate likelihood dating.
+Using partitions and Mixture models for approximate likelihood dating
 ---------------------------------------------------------------------
 
 IQ-TREE supports three partition models for approximate likelihood dating. Under
@@ -129,25 +146,28 @@ Hessian as branches are shared across partitions.
 Since IQ-TREE supports RAxML and NEXUS style partitions input file, you can use
 partitions defined in the following format.
 
-    DNA, part1 = 1-100
-    DNA, part2 = 101-450
-
+```
+DNA, part1 = 1-100
+DNA, part2 = 101-450
+```
 If your partition file is called `example.nex`,
 
-    iqtree -s example.phy  -Q example.nex -m GTR+G4 -te example_tree.nwk --dating mcmctree 
-
+```
+iqtree -s example.phy  -Q example.nex -m GTR+G4 -te example_tree.nwk --dating mcmctree 
+```
 
 Here, IQ-TREE generates the Hessian file using the `GTR+G4` model for all
 partitions. If you need to use different models for each partition, you need to
 create a more flexible NEXUS file like the following.
 
-    #nexus
-    begin sets;
-        charset part1 = 1-100;
-        charset part2 = 101-450;
-        charpartition mine = GTR+G4:part1, HKY:part2;
-    end;
-
+```
+#nexus
+begin sets;
+    charset part1 = 1-100;
+    charset part2 = 101-450;
+    charpartition mine = GTR+G4:part1, HKY:part2;
+end;
+```
 Here, IQ-TREE uses `GTR+G4` model for partition 1, and `HKY` model for partition
 2 respectively. Using `-q` and `-p` options, you can generate the Hessian file
 which considers `edge-linked equal branch partition models` and `edge-linked
@@ -156,12 +176,14 @@ proportional branch length models` respectively.
 IQ-TREE also supports mixture models for the Hessian file generation. You can
 simply specify DNA or Amino Acid Mixture model as following,
 
-    iqtree -s example.phy  -m "MIX{GTR,HKY}+G4" -te example_tree.nwk –-dating mcmctree 
-
+```
+iqtree -s example.phy  -m "MIX{GTR,HKY}+G4" -te example_tree.nwk –-dating mcmctree 
+```
 If you need to use an Amino Acid profile mixture model such as C60 model,
 
-    iqtree -s example.phy  -m LG+G4+C60 -te example_tree.nwk –-dating mcmctree 
-
+```
+iqtree -s example.phy  -m LG+G4+C60 -te example_tree.nwk –-dating mcmctree 
+```
 If you are using ModelFinder or MixtureFinder, you need to follow a two-step
 approach. First, you can estimate the best-fit model for the data using
 ModelFinder or MixtureFinder. Then, the Hessian file can be generated using
@@ -173,8 +195,9 @@ How to run MCMCtree
 You can directly run MCMCtree from the control file generated by IQ-TREE in step
 2. The command to run MCMCtree with the control file is,
 
-    mcmctree example.mcmctree.ctl
-
+```
+mcmctree example.mcmctree.ctl
+```
 
 
 The control file generated by IQ-TREE has the following format. You can simply