update doc

Author: bqminh

doc/Complex-Models.md

@@ -2,7 +2,7 @@
 layout: userdoc
 title: "Complex Models"
 author: 928003585, 95438353+HectorBanos, Dominik Schrempf, Jana Trifinopoulos, Minh Bui, Rob Lanfear, Thomaskf, Trongnhan Uit
-date:    2024-04-18
+date:    2024-07-31
 docid: 11
 icon: book
 doctype: manual
@@ -156,15 +156,17 @@ Here, we estimate the optimal Q mixture model. To select mixture model and then
 
 	iqtree -s example.phy -m MIX+MFP
 
-Likelihood ratio test (LRT) with p-value = 0.05 is the default method to assess the number of classes in the Q mixture model. To change the p-value:
+BIC is the default criterion to assess the number of classes in the Q mixture model. AIC, AICc or likelihood ratio test (LRT) are also available to assess the number of classes.
 
-	iqtree -s example.phy -m MIX+MF -lrt 0.01
+To use AIC:
+
+	iqtree -s example.phy -m MIX+MF -merit AIC
 
-Here, we change the LRT p-value to 0.01. To use information criteria instead of LRT to assess the number of classes:
+To use likelihood ratio test with p-value = 0.05 to assess the number of classes:
 
-	iqtree -s example.phy -m MIX+MF -lrt 0 -merit BIC
+	iqtree -s example.phy -m MIX+MF -lrt 0.05 
 
-Here, `-lrt 0` means turning off the LRT, then `-merit BIC` means using BIC to assess the number of classes. (Note that: `-merit` also decides the creterion for selecting subtitution model type in each classes. If using LRT for assessing the number of classes, the default creterion for selecting subtitution model type is BIC.)
+(Note that: `-merit` also decides the creterion for selecting subtitution model type in each classes. If using LRT for assessing the number of classes, the default creterion for selecting subtitution model type is BIC.)
 
 Options for ModelFinder also work for MixtureFinder, e.g.:
 
@@ -177,7 +179,7 @@ Other options for MixtureFinder:
 | Model option   | Description                                                                                                                          |
 | -------------- | ------------------------------------------------------------------------------------------------------------------------------------ |
 | `-qmax`        | Maximum number of Q-mixture classes (default: 10). Specify a number after the option (e.g., `-qmax 5`).                              |
-| `-mrate-twice` | Whether estimate the rate heterogeneity across sites models again after select the best Q-mixture model. 1: yes, 0: no. (default: 1) |
+| `-mrate-twice` | Whether estimate the rate heterogeneity across sites models again after select the best Q-mixture model. 1: yes, 0: no. (default: 0) |
 
 If you use MixtureFinder in a publication please cite:
 
@@ -415,3 +417,4 @@ Please note that, in any MAST model with more than one substitution model (i.e.
 [Wang et al., 2008]: https://doi.org/10.1186/1471-2148-8-331
 
 
+

doc/iqtree-doc.pdf

@@ -1,14 +1,14 @@
 ---
 layout: workshop
 title: "Perform a Goldman-Cox test"
-author: Rob Lanfear
-date:    2022-06-07
+author: Minh Bui, Rob Lanfear
+date:    2024-07-06
 docid: 100
 ---
 
 # Perform a Goldman-Cox test 
 
-## What's a Goldman-Cox test
+## What is a Goldman-Cox test?
 
 Nick Goldman explains the Goldman-Cox (GC) test in [this paper](https://link.springer.com/article/10.1007/BF00166252)
 

doc/recipes/goldman-cox-test.md

@@ -1,31 +1,30 @@
 ---
 layout: userdoc
 title: "Recipes (How-To)"
-author: Rob Lanfear
-date:    2022-06-07
+author: Minh Bui, Rob Lanfear
+date:    2024-07-06
 docid: 9.5
 icon: question-circle
 doctype: manual
 tags:
 - manual
-description: Collection of one-off examples of analyses in IQ-TREE.
+description: Collection of examples that combine IQ-TREE with other software.
 sections_new_page: True
 sections:
 - name: Phylogenetic placement
   url: phylogenetic-placement
 - name: Perform a Goldman-Cox test 
   url: goldman-cox-test
+- name: Estimating gene, site, and quartet concordance vectors 
+  url: concordance-vector
 ---
 
 # Recipes
 
-This is a collection of one-off examples of analyses in IQ-TREE. 
-<!--more-->
-One might call them "infrequently asked questions". The idea is a searchable and 
-reproducible database of analyses to help the community do what they need to with IQ-TREE.
+This is a collection of detailed examples analyses that combine IQ-TREE with other bits of code and/or software (hence 'recipes'). They are an attempt to go a bit beyond the usual user docs for software, getting closer to end-to-end analyses. The idea is a searchable and reproducible database of analyses to help the community do what they need to with IQ-TREE.
 
-If you'd like to request a recipe, please head over to the issues page and 
-use the 'recipe wanted' label.
+If you'd like to request a recipe, please head over to the issues page and use the 'recipe wanted' label, and describe in as much detail as possible (with references and example data if you can) what it is you would like.
 
 * [How to do phylogenetic placement](phylogenetic-placement)
 * [How to perform a Goldman-Cox test](goldman-cox-test)
+* [Estimating gene, site, and quartet concordance vectors](concordance-vector)