update doc

doc/Compilation-Guide.md

@@ -2,7 +2,7 @@
 layout: userdoc
 title: "Compilation Guide"
 author: Dominik Schrempf, Jana Trifinopoulos, Meaningseeking, Minh Bui, Thomaskf
-date:    2024-04-18
+date:    2024-05-25
 docid: 20
 icon: book
 doctype: manual
@@ -269,7 +269,7 @@ Starting with version 2.3.3, you can compile and create IQ-TREE2 lib file.
 
 If you want to compile the IQ-TREE2 lib file, simply run:
 
-    cmake -DMAKE_LIB=ON ..
+    cmake -DBUILD_LIB=ON ..
     make -j4
 
 

doc/Concordance-Factor.md

@@ -1,8 +1,8 @@
 ---
 layout: userdoc
 title: "Concordance Factor"
-author: Minh Bui, Rob Lanfear
-date:    2022-12-01
+author: Minh Bui, Rob Lanfear, Trongnhan Uit
+date:    2024-05-27
 docid: 6
 icon: info-circle
 doctype: tutorial
@@ -164,9 +164,9 @@ So, suppose that in the first step of the analysis you ran the command as above:
 
 That command will have figured out for you the model of evolution, all the parameters of that model, and the branch lengths of the corresponding tree. We can re-use all of that useful information in the final step. It just takes a little bit of effort to find what you need.
 
-First we'll get the model parameters we need. If you take a look at the end of the `concat.log` file you will find a little section called `ALISIM COMMAND`. You can find it like this on mac/linux (or just open the `concat.log` file in a text editor and scroll to the end:
+First we'll get the model parameters we need. If you take a look at the end of the `concat.iqtree` file you will find a little section called `ALISIM COMMAND`. You can find it like this on mac/linux (or just open the `concat.iqtree` file in a text editor and scroll to the end:
 
-	tail concat.log
+	tail concat.iqtree
 
 You should see something like this:
 
@@ -189,7 +189,7 @@ To put all of that together, we are going to change the final command of the tut
 	# compute site concordance factor using likelihood with v2.2.2
 	iqtree2 -te concat.treefile -s ALN_FILE --scfl 100 --prefix concord2
 
-To one of these, where we add the two extra commands via `-blfix` and `-m`, to fix all the parameters we already calculated. A reminder - do NOT use the exact commandlines above. You have to replace everything after the `-m` with what you found in your own `concat.log` file:
+To one of these, where we add the two extra commands via `-blfix` and `-m`, to fix all the parameters we already calculated. A reminder - do NOT use the exact commandlines above. You have to replace everything after the `-m` with what you found in your own `concat.iqtree` file:
 
 	# faster analysis, using pre-computed model parameters, with per-locus alignments
 	# compute site concordance factor using likelihood with v2.2.2

doc/Rootstrap.md

@@ -2,7 +2,7 @@
 layout: userdoc
 title: "Rooting phylogenies"
 author: Minh Bui, Suha Naser
-date:    2021-05-18
+date:    2024-06-07
 docid: 8
 icon: info-circle
 doctype: tutorial
@@ -107,12 +107,12 @@ as the run above to infer an unrooted tree using reversible models:
 
 This run will also write the best partitioning scheme to `rev_dna.best_scheme.nex` file.
 In the second step, we will re-use this best scheme but replace the substitution model 
-with the most general non-reversible DNA model, 12.12 or UNREST 
+with the most general non-reversible DNA model, UNREST or 12.12
 (see [this doc](Substitution-Models#lie-markov-models)) to obtain a rooted tree:
 
-    iqtree2 -s bovidae.phy -p rev_dna.best_scheme.nex --model-joint 12.12 -B 1000 -T AUTO --prefix nonrev_dna
+    iqtree2 -s bovidae.phy -p rev_dna.best_scheme.nex --model-joint UNREST -B 1000 -T AUTO --prefix nonrev_dna
 
-The option `--model-joint 12.12` tells IQ-TREE use a linked substitution model 12.12 across
+The option `--model-joint UNREST` tells IQ-TREE use a linked substitution model UNREST across
 all partitions. This is to avoid potential over-parameterization as this is very 
 parameter-rich model with 12 parameters.