add new pdf and script to build it

Author: bqminh

doc/Back.md

@@ -0,0 +1,14 @@
+
+---
+title: |
+    IQ-TREE version 3.0.0 - Tutorials and Manual
+    Phylogenomic software by maximum likelihood
+    
+subtitle: "<http://www.iqtree.org>"
+author: |
+    Bui Quang Minh, Rob Lanfear, Thomas Wong, Nhan Ly-Trong\
+    Jana Trifinopoulos, Dominik Schrempf, Heiko A. Schmidt
+
+date: May 2, 2025
+---
+

doc/Compilation-Guide.md

@@ -338,3 +338,4 @@ Many developers in MacOS use Xcode to develop the code. To generate an XCode pro
     cmake -G Xcode <IQTREE_SOURCE_DIR>
 
 This will generate a a subfolder `build-xcode/iqtree.xcodeproj`, which you can open in Xcode now.
+

doc/Frequently-Asked-Questions.md

@@ -331,3 +331,4 @@ iqtree3 -p FOLDER_NAME --out-aln OUTFILE_NAME --out-format NEXUS
 ```
 
 would output the alignment in nexus format.
+

doc/Front.md

@@ -1,15 +1,5 @@
 ---
 layout: userdoc
-title: |
-    IQ-TREE version 2.2.0: Tutorials and Manual
-    Phylogenomic software by maximum likelihood
-    
-subtitle: "<http://www.iqtree.org>"
-author: |
-    Bui Quang Minh, Rob Lanfear, Nhan Ly-Trong\
-    Jana Trifinopoulos, Dominik Schrempf, Heiko A. Schmidt
-
-date: March 25, 2022
 keywords: [phylogenomic inference, maximum likelihood]
 toc: true
 papersize: A4

doc/build-doc.sh

@@ -0,0 +1,13 @@
+#! /bin/bash
+
+dest_dir="."
+
+files="Front.md Home.md Quickstart.md Web-Server-Tutorial.md Tutorial.md Advanced-Tutorial.md Assessing-Phylogenetic-Assumptions.md Concordance-Factor.md Dating.md Rootstrap.md AliSim.md Command-Reference.md Substitution-Models.md Complex-Models.md Polymorphism-Aware-Models.md Compilation-Guide.md Frequently-Asked-Questions.md Back.md"
+
+#generate pdf
+cd $dest_dir
+pdf="iqtree-doc.pdf"
+cat $files | sed 's/]([a-zA-Z\-]*#/](#/g' | sed 's/(Quickstart)/(#getting-started)/g' | sed 's/(Web-Server-Tutorial)/(#web-server-tutorial)/g' |  sed 's/(Tutorial)/(#beginners-tutorial)/g' | sed 's/(Advanced-Tutorial)/(#advanced-tutorial)/g' | sed 's/(Command-Reference)/(#command-reference)/g' | sed 's/(Substitution-Models)/(#substitution-models)/g' | sed 's/(Complex-Models)/(#complex-models)/g' | sed 's/(Polymorphism-Aware-Models)/(#polymorphism-aware-models)/g' | sed 's/(Compilation-Guide)/(#compilation-guide)/g' | sed 's/(Frequently-Asked-Questions)/(#frequently-asked-questions)/g' | sed 's/{:.*}//g' > iqtree-doc.md
+pandoc iqtree-doc.md --number-sections --listings --pdf-engine=xelatex -o $pdf
+echo "Generated $dest_dir/$pdf"
+rm iqtree-doc.md