### Install Example Data Files

Source: https://github.com/iqtree/iqtree3/blob/master/CMakeLists.txt

Installs example data files (.nex, .phy, .cf) from the 'example' directory to the root of the installation destination.

```cmake
install (FILES "${PROJECT_SOURCE_DIR}/example/models.nex" DESTINATION .)
install (FILES "${PROJECT_SOURCE_DIR}/example/example.phy" DESTINATION .)
install (FILES "${PROJECT_SOURCE_DIR}/example/example.nex" DESTINATION .)
install (FILES "${PROJECT_SOURCE_DIR}/example/example.cf" DESTINATION .)
```

--------------------------------

### Run IQ-TREE Example (Windows)

Source: https://github.com/iqtree/iqtree3/wiki/Quickstart

Execute a basic IQ-TREE analysis with an example alignment file on Windows.

```bash
bin\iqtree -s example.phy
```

--------------------------------

### Install IQ-TREE 3 Executables

Source: https://github.com/iqtree/iqtree3/blob/master/CMakeLists.txt

Installs the main 'iqtree3' executable and 'iqtree3-aa' if enabled, to the 'bin' directory. Also installs the 'click' variants of these executables on Windows.

```cmake
install (TARGETS iqtree3 DESTINATION bin)
if (USE_CMAPLE_AA STREQUAL "ON")
	install (TARGETS iqtree3-aa DESTINATION bin)
endif()

if (WIN32)
    install (FILES "${BINARY_DIR}/iqtree3${EXE_SUFFIX}-click.exe" DESTINATION bin)
    if (USE_CMAPLE_AA STREQUAL "ON")
    	install (FILES "${BINARY_DIR}/iqtree3-aa${EXE_SUFFIX}-click.exe" DESTINATION bin)
    endif()
endif()
```

--------------------------------

### General Install Settings

Source: https://github.com/iqtree/iqtree3/blob/master/yaml-cpp/CMakeLists.txt

Defines the installation directories for include files and libraries. The library installation directory is dynamically set based on the LIB_SUFFIX variable.

```cmake
set(INCLUDE_INSTALL_ROOT_DIR include)

set(INCLUDE_INSTALL_DIR ${INCLUDE_INSTALL_ROOT_DIR}/yaml-cpp)
set(LIB_INSTALL_DIR "lib${LIB_SUFFIX}")

set(_INSTALL_DESTINATIONS
	RUNTIME DESTINATION bin
	LIBRARY DESTINATION ${LIB_INSTALL_DIR}
	ARCHIVE DESTINATION ${LIB_INSTALL_DIR}
)


###
### Library
###
```

--------------------------------

### Install IQ-TREE on FreeBSD

Source: https://github.com/iqtree/iqtree3/wiki/Quickstart

Use this command to install IQ-TREE on FreeBSD systems.

```bash
pkg install iqtree
```

--------------------------------

### Run IQ-TREE Example (Mac OS X)

Source: https://github.com/iqtree/iqtree3/wiki/Quickstart

Execute a basic IQ-TREE analysis with an example alignment file on Mac OS X.

```bash
bin/iqtree -s example.phy
```

--------------------------------

### Install IQ-TREE2, ASTRAL-III, and R Packages

Source: https://github.com/iqtree/iqtree3/wiki/recipes/concordance-vector

Sets up a conda environment and installs necessary software and R packages for estimating concordance vectors. Ensure you have conda installed and configured.

```bash
conda create --name concordance
conda activate concordance
conda install -c bioconda iqtree astral-tree
conda install -c conda-forge r-base r-tidyverse r-boot r-ape r-ggtext
```

--------------------------------

### Install IQ-TREE with Homebrew

Source: https://github.com/iqtree/iqtree3/wiki/Quickstart

Install IQ-TREE version 3 using Homebrew on macOS or Linux.

```bash
brew install brewsci/bio/iqtree3
```

--------------------------------

### NEXUS Partition File Example

Source: https://github.com/iqtree/iqtree3/wiki/Advanced-Tutorial

Example of a NEXUS partition file defining character sets and partitions with specific substitution models.

```nexus
#nexus
begin sets;
    charset part1 = 1-100;
    charset part2 = 101-384;
    charpartition mine = HKY+G:part1, GTR+I+G:part2;
end;
```

--------------------------------

### Basic CMakeLists.txt Setup

Source: https://github.com/iqtree/iqtree3/blob/master/yaml-cpp/util/CMakeLists.txt

Sets the minimum CMake version required and adds source files for a target. Use this to define the build environment for your project.

```cmake
cmake_minimum_required(VERSION 3.5)

add_sources(parse.cpp)
add_executable(parse parse.cpp)
target_link_libraries(parse yaml-cpp)
```

--------------------------------

### Install IQ-TREE with Anaconda

Source: https://github.com/iqtree/iqtree3/wiki/Quickstart

Install IQ-TREE using the bioconda channel with Anaconda.

```bash
conda install -c bioconda iqtree
```

--------------------------------

### Install IQ-TREE on Debian Linux

Source: https://github.com/iqtree/iqtree3/wiki/Quickstart

Use this command to install IQ-TREE on Debian-based Linux distributions.

```bash
sudo apt-get install iqtree
```

--------------------------------

### Define Installation Directories

Source: https://github.com/iqtree/iqtree3/blob/master/zlib-1.2.7/CMakeLists.txt

Configures cache variables for installation directories for executables, libraries, headers, man pages, and pkgconfig files.

```cmake
set(INSTALL_BIN_DIR "${CMAKE_INSTALL_PREFIX}/bin" CACHE PATH "Installation directory for executables")
set(INSTALL_LIB_DIR "${CMAKE_INSTALL_PREFIX}/lib" CACHE PATH "Installation directory for libraries")
set(INSTALL_INC_DIR "${CMAKE_INSTALL_PREFIX}/include" CACHE PATH "Installation directory for headers")
set(INSTALL_MAN_DIR "${CMAKE_INSTALL_PREFIX}/share/man" CACHE PATH "Installation directory for manual pages")
set(INSTALL_PKGCONFIG_DIR "${CMAKE_INSTALL_PREFIX}/share/pkgconfig" CACHE PATH "Installation directory for pkgconfig (.pc) files")
```

--------------------------------

### Install Pkgconfig File on UNIX

Source: https://github.com/iqtree/iqtree3/blob/master/yaml-cpp/CMakeLists.txt

Configures and installs the yaml-cpp.pc file for pkgconfig on UNIX-like systems when YAML_CPP_INSTALL is enabled.

```cmake
if(UNIX)
	set(PC_FILE ${CMAKE_BINARY_DIR}/yaml-cpp.pc)
	configure_file("yaml-cpp.pc.cmake" ${PC_FILE} @ONLY)
	install(FILES ${PC_FILE} DESTINATION ${LIB_INSTALL_DIR}/pkgconfig)
endif()
```

--------------------------------

### Run IQ-TREE with PMSF model and guide tree

Source: https://github.com/iqtree/iqtree3/wiki/Complex-Models

Use this command to run IQ-TREE with a PMSF model, specifying a guide tree obtained from a simpler model analysis.

```bash
iqtree -s <alignment> -m LG+C20+F+G -ft <guide_tree>
```

--------------------------------

### Setup Clang-Tidy

Source: https://github.com/iqtree/iqtree3/blob/master/terraphast/CMakeLists.txt

Finds the clang-tidy executable and sets up a command line for it, including specific checks and the fix option. This is used for static analysis of the code.

```cmake
find_program(CLANG_TIDY_PATH NAMES "clang-tidy")
if(NOT CLANG_TIDY_PATH)
    message(STATUS "clang-tidy not found.")
else()
    message(STATUS "clang-tidy found: ${CLANG_TIDY_PATH}")
    set(CLANG_TIDY_COMMANDLINE "${CLANG_TIDY_PATH}" "-checks=llvm-namespace-comment -fix")
endif()
```

--------------------------------

### Install yaml-cpp Target and Headers

Source: https://github.com/iqtree/iqtree3/blob/master/yaml-cpp/CMakeLists.txt

Installs the yaml-cpp target and its header files when YAML_CPP_INSTALL is enabled.

```cmake
install(TARGETS yaml-cpp EXPORT yaml-cpp-targets ${_INSTALL_DESTINATIONS})
	install(
		DIRECTORY ${header_directory}
		DESTINATION ${INCLUDE_INSTALL_DIR}
		FILES_MATCHING PATTERN "*.h"
	)
```

--------------------------------

### Running IQ-TREE with a Specified Number of CPU Cores

Source: https://github.com/iqtree/iqtree3/wiki/workshop/molevol2018

This example demonstrates how to use the -nt option to specify the number of CPU cores for IQ-TREE analysis. It's recommended for long alignments to speed up computation.

```bash
iqtree -s example.phy -m TIM2+I+G -nt 2
```

--------------------------------

### IQ-TREE Command Line for Phylogenetic Placement

Source: https://github.com/iqtree/iqtree3/wiki/recipes/phylogenetic-placement

This example shows a typical command-line invocation for IQ-TREE, likely used for phylogenetic placement. It includes options for tree building and outputting results.

```bash
# IQ-TREE command line example
# This is a placeholder for an actual command. The provided text only contains a tree visualization and scale bar, not a runnable command.
# Example: iqtree -s alignment.fasta -pre output -bb 1000 -alrt 1000
```

--------------------------------

### Install Catch Dependency

Source: https://github.com/iqtree/iqtree3/blob/master/terraphast/documentation/Dependencies.md

This command installs the Catch dependency, which is required for the project. Ensure it is in the default include path.

```bash
catch
```

--------------------------------

### Install IQ-TREE 2 and AMAS using Conda

Source: https://github.com/iqtree/iqtree3/wiki/recipes/Simulating-concatenated-alignments-with-multiple-trees

Set up a fresh environment and install IQ-TREE 2 and AMAS for simulating alignments.

```bash
# set up a fresh environment and activate it
conda create --name simaln
conda activate simaln

# install what we need for this recipe
conda install -c bioconda iqtree amas 
```

--------------------------------

### Install OpenMPI on macOS using Homebrew

Source: https://github.com/iqtree/iqtree3/wiki/Compilation-Guide

Install the OpenMPI library on macOS using the Homebrew package manager. This is a prerequisite for compiling the MPI version of IQ-TREE.

```bash
brew install openmpi
```

--------------------------------

### Automatic CPU Core Detection for IQ-TREE

Source: https://github.com/iqtree/iqtree3/wiki/workshop/molevol2018

This example shows how to use '-nt AUTO' to let IQ-TREE automatically determine the optimal number of CPU cores for the analysis, optimizing performance and efficiency.

```bash
iqtree -s example.phy -m TIM2+I+G -nt AUTO
```

--------------------------------

### Run IQ-TREE with PMSF model, guide tree, and bootstrap

Source: https://github.com/iqtree/iqtree3/wiki/Complex-Models

Perform nonparametric bootstrap analysis under complex models like PMSF by providing a guide tree and specifying the number of bootstrap replicates.

```bash
iqtree -s <alignment> -m LG+C20+F+G -ft <guide_tree> -b 100
```

--------------------------------

### Perform Constrained Search (Example 2)

Source: https://github.com/iqtree/iqtree3/wiki/Advanced-Tutorial

Performs a phylogenetic search with a different topological constraint defined in `example.constr2`. Use `--prefix` for IQ-TREE v3+ or `-pre` for v1.x.

```bash
iqtree -s example.phy -m TIM2+I+G -g example.constr2 --prefix example.constr2
# for version 1.x change --prefix to -pre
```

--------------------------------

### zpipe Usage Example

Source: https://github.com/iqtree/iqtree3/blob/master/zlib-1.2.7/examples/zlib_how.html

This snippet shows the command-line usage for the zpipe utility, which is a simple example program for zlib. It indicates how to specify decompression with the -d flag.

```c
#define SET_BINARY_MODE(file)

    }

    /* otherwise, report usage */
    else {
        fputs("zpipe usage: zpipe [-d] < source > dest\n", stderr);
        return 1;
    }
}
```

--------------------------------

### zlib Usage Example Header

Source: https://github.com/iqtree/iqtree3/blob/master/zlib-1.2.7/examples/zlib_how.html

This snippet includes the necessary header files for zlib operations and standard I/O functions. It is essential for using zlib's compression and decompression capabilities.

```c
#include <stdio.h>
#include <string.h>
#include <assert.h>
#include "zlib.h"
```

--------------------------------

### Start zlib Compression Loop

Source: https://github.com/iqtree/iqtree3/blob/master/zlib-1.2.7/examples/zlib_how.html

Begins the main compression loop, which continues until the end of the input file is reached. This loop contains the primary call to the `deflate` function.

```c
    /* compress until end of file */
    do {

```

--------------------------------

### Perform Constrained Search (Example 3)

Source: https://github.com/iqtree/iqtree3/wiki/Advanced-Tutorial

Performs a phylogenetic search with a third topological constraint defined in `example.constr3`. Use `--prefix` for IQ-TREE v3+ or `-pre` for v1.x.

```bash
iqtree -s example.phy -m TIM2+I+G -g example.constr3 --prefix example.constr3
# for version 1.x change --prefix to -pre
```

--------------------------------

### Simulate alignment and build example tree

Source: https://github.com/iqtree/iqtree3/wiki/recipes/phylogenetic-placement

This script simulates an alignment, checks sequence names, replaces specific names to simulate new sequences, prunes them from a tree, and then runs IQ-TREE to add them back. It requires Unix environment and newick_utils.

```bash
# simulate an alignment of 20 sequences (set the seed for reproducibility only)
iqtree3 --alisim sequences -t RANDOM{yh/20} -seed 438579088 -af fasta -m JC

# check the names
grep '>' sequences.fa

# replace names of 3 of them to be 'NEW_N'
sed -i -e 's/T18/NEW_1/g' sequences.fa
sed -i -e 's/T19/NEW_2/g' sequences.fa
sed -i -e 's/T20/NEW_3/g' sequences.fa

# check the names again
grep '>' sequences.fa

# prune the NEW_N sequences from the tree using newick_utils
nw_prune sequences.treefile T18 T19 T20 > existing_tree.nex

# check that you have the files you need
ls -lh

# run IQ-TREE to add NEW_N seqs back
iqtree -g existing_tree.nex -s sequences.fa -pre seqs_added -seed 438579088

# optional: do a global re-optimisation of the tree, using previous tree as start
iqtree -s sequences.fa -t seqs_added.treefile -pre re_optimised -seed 438579088
```

--------------------------------

### Basic Gentrius Analysis with Presence-Absence Matrix

Source: https://github.com/iqtree/iqtree3/blob/master/terrace/README.md

Use this command to start a Gentrius analysis using a phylogenetic tree file and a species per locus presence-absence matrix.

```bash
iqtree2 -gentrius <file 1> -pr_ab_matrix <file 2>
```

--------------------------------

### Show All Available Options

Source: https://github.com/iqtree/iqtree3/wiki/Quickstart

Display a help message listing all available command-line options for IQ-TREE.

```bash
iqtree -h
```

--------------------------------

### General Compilation Settings and Platform Specifics

Source: https://github.com/iqtree/iqtree3/blob/master/yaml-cpp/CMakeLists.txt

Sets up general compilation flags and platform-specific configurations for Windows DLLs and installation prefixes. It also handles architecture settings for Apple and iPhone builds.

```cmake
set(yaml_c_flags ${CMAKE_C_FLAGS})
set(yaml_cxx_flags ${CMAKE_CXX_FLAGS})

if(BUILD_SHARED_LIBS)
	set(LABEL_SUFFIX "shared")
else()
	set(LABEL_SUFFIX "static")
endif()

if(APPLE)
	if(APPLE_UNIVERSAL_BIN)
		set(CMAKE_OSX_ARCHITECTURES ppc;i386)
	endif()
endif()

if(IPHONE)
	set(CMAKE_OSX_SYSROOT "iphoneos4.2")
	set(CMAKE_OSX_ARCHITECTURES "armv6;armv7")
endif()

if(WIN32)
	if(BUILD_SHARED_LIBS)
		add_definitions(-D${PROJECT_NAME}_DLL) # use or build Windows DLL
	endif()
	if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
		set(CMAKE_INSTALL_PREFIX "C:/")
	endif()
endif()
```

--------------------------------

### Install zlibstatic Library

Source: https://github.com/iqtree/iqtree3/blob/master/zlib-1.2.7/CMakeLists.txt

Installs the zlibstatic library to the appropriate runtime, archive, and library directories based on predefined installation variables. This is conditional on SKIP_INSTALL_LIBRARIES and SKIP_INSTALL_ALL not being set.

```cmake
if (NOT SKIP_INSTALL_LIBRARIES) 
	set(SKIP_INSTALL_LIBRARIES "1")
endif()

if(NOT SKIP_INSTALL_LIBRARIES AND NOT SKIP_INSTALL_ALL )
    #install(TARGETS zlib zlibstatic
    #    RUNTIME DESTINATION "${INSTALL_BIN_DIR}"
    #    ARCHIVE DESTINATION "${INSTALL_LIB_DIR}"
    #    LIBRARY DESTINATION "${INSTALL_LIB_DIR}" )
            install(TARGETS zlibstatic
        RUNTIME DESTINATION "${INSTALL_BIN_DIR}"
        ARCHIVE DESTINATION "${INSTALL_LIB_DIR}"
        LIBRARY DESTINATION "${INSTALL_LIB_DIR}" )
endif()
```

--------------------------------

### Create Build Directory and Navigate

Source: https://github.com/iqtree/iqtree3/wiki/Compilation-Guide

Create a separate directory for building the project to keep the source tree clean, and then change into this new directory.

```bash
mkdir build
cd build
```

--------------------------------

### Simulating with Root Sequence Frequencies and Custom Model

Source: https://github.com/iqtree/iqtree3/wiki/AliSim

This example demonstrates simulating an alignment where the root sequence is generated with user-specified state frequencies and a custom model. Subsequent nodes use the specified model and frequencies, while other branches default to the Juke-Cantor model.

```text
(A:0.1,(B:0.1,C:0.2),(D:0.3,E:0.1):0.2):0.3[&model=GTR,freqs=0.2/0.3/0.1/0.4];
```

--------------------------------

### Topology-Unlinked Partition Model Example

Source: https://github.com/iqtree/iqtree3/wiki/AliSim

Prepare a Newick file with multiple trees, one for each partition, allowing independent topologies and branch lengths. This is useful when gene trees differ significantly.

```newick
(A:0.1,(B:0.26,C:0.15):0.1,D:0.05);
(A:0.2,B:0.1,C:0.3);
(A:0.05,B:0.03,(C:0.21,D:0.22):0.21);
((A:0.24,B:0.14):0.19,C:0.07,D:0.1);
((A:0.1,C:0.1):0.04,B:0.4,D:0.5);

```

--------------------------------

### Running IQ-TREE with Partition File

Source: https://github.com/iqtree/iqtree3/wiki/Advanced-Tutorial

Initiate IQ-TREE using a NEXUS file that defines partition schemes. For IQ-TREE version 1.x, use -spp instead of -p.

```bash
iqtree -p example.nex
    # for version 1.x change -p to -spp
```

--------------------------------

### Ultrafast Bootstrap with Partition Model (Site Resampling)

Source: https://github.com/iqtree/iqtree3/wiki/Advanced-Tutorial

Perform ultrafast bootstrapping with partition models, resampling sites within partitions. For IQ-TREE version 1.x, use -spp, -bb, and -bsam.

```bash
iqtree -s example.phy -p example.nex -B 1000
    # for version 1.x change -p to -spp and -B to -bb
```

--------------------------------

### Determine Install Cmake Directory

Source: https://github.com/iqtree/iqtree3/blob/master/yaml-cpp/CMakeLists.txt

Sets the installation directory for CMake configuration files based on the operating system.

```cmake
if(WIN32 AND NOT CYGWIN)
	set(INSTALL_CMAKE_DIR CMake)
else()
	set(INSTALL_CMAKE_DIR ${LIB_INSTALL_DIR}/cmake/yaml-cpp)
endif()
```

--------------------------------

### Install CMake Configuration Files and Exported Targets

Source: https://github.com/iqtree/iqtree3/blob/master/yaml-cpp/CMakeLists.txt

Installs the CMake configuration files and exported targets when YAML_CPP_INSTALL is enabled.

```cmake
install(FILES
	"${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/yaml-cpp-config.cmake"
	"${PROJECT_BINARY_DIR}/yaml-cpp-config-version.cmake"
	DESTINATION "${INSTALL_CMAKE_DIR}" COMPONENT dev)
install(EXPORT yaml-cpp-targets DESTINATION ${INSTALL_CMAKE_DIR})
```

--------------------------------

### Configure 32-bit IQ-TREE build on Windows

Source: https://github.com/iqtree/iqtree3/wiki/Compilation-Guide

For Windows, when building the 32-bit version, specify the i686 target architecture and use MinGW Makefiles.

```bash
cmake -G "MinGW Makefiles" -DCMAKE_C_FLAGS=--target=i686-pc-windows-gnu -DCMAKE_CXX_FLAGS=--target=i686-pc-windows-gnu -DCMAKE_MAKE_PROGRAM=mingw32-make ..
```

--------------------------------

### Running IQ-TREE with Tip Dates for Time Tree Reconstruction

Source: https://github.com/iqtree/iqtree3/wiki/Dating

This command initiates IQ-TREE to perform model selection, ML tree inference, and time tree construction using tip dates. It requires the sequence alignment file and the prepared date file.

```bash
iqtree -s ALN_FILE --date DATE_FILE
```

--------------------------------

### Install DLLs for Non-Single-Threaded Builds on Windows

Source: https://github.com/iqtree/iqtree3/blob/master/CMakeLists.txt

Installs pthread and libiomp5md DLLs to the 'bin' directory on Windows for non-single-threaded builds, specifically when using MSVC or Clang.

```cmake
if (WIN32)
    if (NOT IQTREE_FLAGS MATCHES "single" AND MSVC)
        install(FILES  "${PROJECT_SOURCE_DIR}/lib/pthreadVC2.dll" DESTINATION bin)
        install(FILES  "${PROJECT_SOURCE_DIR}/lib/libiomp5md.dll" DESTINATION bin)
    endif()

    if (NOT IQTREE_FLAGS MATCHES "single" AND CLANG)
        install(FILES  "${PROJECT_SOURCE_DIR}/lib/libiomp5md.dll" DESTINATION bin)
    endif()

endif()
```

--------------------------------

### Configure 32-bit multicore IQ-TREE build

Source: https://github.com/iqtree/iqtree3/wiki/Compilation-Guide

To build the 32-bit multicore version, include both 'omp' and 'm32' in the IQTREE_FLAGS.

```bash
cmake -DIQTREE_FLAGS=omp-m32 ..
```

--------------------------------

### Run IQ-TREE 2 from command line

Source: https://github.com/iqtree/iqtree3/wiki/workshop/molevol2022

Invokes the IQ-TREE 2 executable from the command line. Ensure the IQ-TREE binary is in your system's PATH.

```bash
iqtree2
```

--------------------------------

### Create Static Library on Unix Systems

Source: https://github.com/iqtree/iqtree3/blob/master/CMakeLists.txt

Creates a static library 'libiqtree.a' on Unix systems by unifying static libraries and then removing a potentially conflicting 'libiqtree3.a'. It uses a helper script for library unification.

```cmake
elseif(UNIX)
        add_custom_command(
            TARGET iqtree3 POST_BUILD
            COMMAND mkdir all_libs
            COMMAND ln -s ${STATIC_LIBS} all_libs
            COMMAND ${PROJECT_SOURCE_DIR}/test_scripts/unify-static-libs.sh libiqtree.a all_libs
            COMMAND rm -rf all_libs
            COMMAND rm libiqtree3.a
            VERBATIM)
```

--------------------------------

### NEXUS Cluster File Example

Source: https://github.com/iqtree/iqtree3/wiki/Command-Reference

An example of a NEXUS file format for defining taxon clusters for likelihood mapping analysis. Sequences are grouped into named sets.

```nexus
#NEXUS
begin sets;
    taxset Cluster1 = A B C;
    taxset Cluster2 = D E;
    taxset Cluster3 = F G H I;
    taxset Cluster4 = J;
    taxset IGNORED = X;
end;
```

--------------------------------

### Example Simulated Alignment Output

Source: https://github.com/iqtree/iqtree3/wiki/AliSim

This is an example of the output format for a simulated multiple sequence alignment, showing the number of sequences, number of sites, and the aligned sequences.

```text
4 1000
A       AAATTTGGTCCTGTGATTCAGCAGTGAT...
B       CTTCCACACCCCAGGACTCAGCAGTGAT...
C       CTACCACACCCCAGGACTCAGCAGTAAT...
D       CTACCACACCCCAGGAAACAGCAGTGAT...
```

--------------------------------

### Run second phase of PMSF model analysis using .sitefreq file

Source: https://github.com/iqtree/iqtree3/wiki/Complex-Models

Run the second phase of the PMSF model analysis on a low-memory machine by providing the alignment and the pre-computed .sitefreq file.

```bash
iqtree -s <alignment> -m LG+C20+F+G -fs <file.sitefreq> -b 100
```

--------------------------------

### Configure IQ-TREE with MPI compiler wrappers

Source: https://github.com/iqtree/iqtree3/wiki/Compilation-Guide

Alternatively, configure the build by explicitly specifying the MPI C and C++ compiler wrappers.

```bash
cmake -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx ..
make -j4
```

--------------------------------

### Example Amino Acid Substitution Matrix (Q.plant)

Source: https://github.com/iqtree/iqtree3/wiki/Estimating-amino-acid-substitution-models

This is an example of the extracted Q.plant file, which contains the lower diagonal part of the AA exchange rates matrix and 20 AA frequencies in PAML format.

```text
0.120955
0.048462 0.458565
0.436023 0.037551 4.799928
0.470505 1.707355 0.338537 0.000100
0.261114 3.736017 0.605443 0.147890 0.286279
0.837596 0.016734 0.388965 5.815020 0.000100 4.138646
1.939708 1.199364 0.911021 1.413132 0.681747 0.419571 0.886564
```

--------------------------------

### Global re-optimization of a tree

Source: https://github.com/iqtree/iqtree3/wiki/recipes/phylogenetic-placement

Re-optimize an existing tree without constraints using the -t option to set the starting tree and -s for the alignment. This command starts from the best available tree estimate and further optimizes it.

```bash
iqtree -s sequences.fa -t sequences.treefile -pre reoptimised
```

--------------------------------

### Ancestral State Reconstruction Example

Source: https://github.com/iqtree/iqtree3/wiki/Command-Reference

Example command to perform ancestral state reconstruction using the JC+G model and ASR. The output file contains detailed information about ancestral states and their probabilities for each node and site.

```bash
iqtree -s example.phy -m JC+G -asr
```

```text
# Ancestral state reconstruction for all nodes in example.phy.treefile
# This file can be read in MS Excel or in R with command:
#   tab=read.table('example.phy.state',header=TRUE)
# Columns are tab-separated with following meaning:
#   Node:  Node name in the tree
#   Site:  Alignment site ID
#   State: Most likely state assignment
#   p_X:   Posterior probability for state X (empirical Bayesian method)
Node	Site	State	p_A	p_C	p_G	p_T
Node2	1	C	0.00004	0.99992	0.00002	0.00002
Node2	2	A	0.92378	0.00578	0.00577	0.06468
Node2	3	A	0.95469	0.02634	0.00675	0.01222
Node2	4	C	0.00002	0.99992	0.00002	0.00004
...
```

--------------------------------

### Running IQ-TREE with RAxML/NEXUS Partitions

Source: https://github.com/iqtree/iqtree3/wiki/Dating

Executes IQ-TREE using a specified partition file and a single model for all partitions.

```bash
iqtree -s example.phy  -Q example.nex -m GTR+G4 -te example_tree.nwk --dating mcmctree 
```

--------------------------------

### Adding CMaple Subdirectory

Source: https://github.com/iqtree/iqtree3/blob/master/CMakeLists.txt

Adds the 'cmaple' subdirectory to the build if USE_CMAPLE is ON. It also forces the installation of googletest to be OFF.

```cmake
if (USE_CMAPLE STREQUAL "ON")
	SET(INSTALL_CMAPLE OFF CACHE BOOL "Disable installation of googletest" FORCE)
	add_subdirectory(cmaple)
endif()
```

--------------------------------

### Compile IQ-TREE with Make

Source: https://github.com/iqtree/iqtree3/wiki/Compilation-Guide

Compile the source code using the 'make' command. The '-j' option utilizes all available CPU cores to speed up the compilation process.

```bash
make -j
```

--------------------------------

### Basic Gentrius Analysis with Subtree Set

Source: https://github.com/iqtree/iqtree3/blob/master/terrace/README.md

Start a Gentrius analysis by providing a file containing a set of subtrees.

```bash
iqtree2 -gentrius <file 5>
```

--------------------------------

### Example Assertion Failure Message

Source: https://github.com/iqtree/iqtree3/wiki/Frequently-Asked-Questions

When reporting a bug, provide the assertion message if it appears on the screen. This helps developers pinpoint the issue.

```text
iqtree: ....cpp:140: ...: Assertion '...' failed.
```

--------------------------------

### Set Target Include Directories

Source: https://github.com/iqtree/iqtree3/blob/master/yaml-cpp/CMakeLists.txt

Configures include directories for the yaml-cpp target, differentiating between build and install interfaces, and private build includes.

```cmake
target_include_directories(yaml-cpp
        PUBLIC $<BUILD_INTERFACE:${YAML_CPP_SOURCE_DIR}/include>
               $<INSTALL_INTERFACE:${INCLUDE_INSTALL_ROOT_DIR}>
        PRIVATE $<BUILD_INTERFACE:${YAML_CPP_SOURCE_DIR}/src>)
```

--------------------------------

### Simulating with Edge-Proportional Partitions

Source: https://github.com/iqtree/iqtree3/wiki/AliSim

Initiate simulation using the '--alisim partition' command with the '-p' option for edge-proportional models. This ensures gene-specific rates are applied.

```bash
iqtree3 --alisim partition -p multi_genes.nex -t tree.nwk
```

--------------------------------

### Partitioned Analysis with RAxML-style File

Source: https://github.com/iqtree/iqtree3/wiki/Advanced-Tutorial

Run a partitioned analysis using a RAxML-style partition file. All partitions will use the same rate heterogeneity model specified in the -m option.

```bash
iqtree -s example.phy -p example.partitions -m GTR+I+G
# for version 1.x change -p to -spp
```

--------------------------------

### Constraint Tree Topology Example

Source: https://github.com/iqtree/iqtree3/wiki/Advanced-Tutorial

A sample constraint tree in NEWICK format, defining topological relationships between species for constrained tree searches.

```newick
((Human,Seal),(Cow,Whale));
```

--------------------------------

### Starting the Deflate Loop

Source: https://github.com/iqtree/iqtree3/blob/master/zlib-1.2.7/examples/zlib_how.html

Initiates the do-while loop for processing input data with the deflate function until the output buffer is full or compression is finished.

```c
/* run deflate() on input until output buffer not full, finish
   compression if all of source has been read in */
do {
```

--------------------------------

### Configure IQ-TREE with CMake

Source: https://github.com/iqtree/iqtree3/wiki/Compilation-Guide

Use CMake to configure the build process. This command should be run from the build directory, pointing to the source directory with '..'.

```bash
cmake ..

```

--------------------------------

### MCMCtree Control File Configuration

Source: https://github.com/iqtree/iqtree3/wiki/Dating

Example configuration for an MCMCtree control file, specifying parameters for MCMC runs, data types, and evolutionary models.

```plaintext
seed = -1                        * The computer’s current time is used when seed < 0.
seqfile = example.dummy.phy      * A dummy alignment only allow to run MCMCtree
treefile = example.rooted.nwk    * Rooted newick tree with annotated fossil/tip dates
mcmcfile = example.mcmctree.log  * MCMC log of parameters that can be examined in Tracer
outfile = example.mcmctree.out   * Output of the summarized results of MCMCtree
ckpfile = example..mcmctree.ckp         * Checkpoint file of MCMCtree
lessianfile = example.mcmctree.hessian  * File with gradient and hessian matrix

checkpoint = 1  * 0: nothing; 1 : save; 2: resume
ndata = 1       * number of partitions
seqtype = 0     * 0 : nucleotides; 1: codons; 2: AAs (not required if the approximate likelihood method is used)
usedata = 2     * 0: sampling from priors with no data; 1: exact slow likelihood; 2: approximate likelihood
clock = 2       * 1: global clock with equal rates; 2: independent rates; 3: correlated rates
RootAge = <1.0  * safe constraint on root age, used if no fossil for root in the rooted tree file.

BDparas = 1,1,0.5    * birth-rate, death rate, sampling priors for sampling times
finetune = 1: 0.1  0.1  0.1  0.01 .5  * auto (0 or 1) : times, musigma2, rates, mixing, paras, FossilErr
print = 1            * 1: normal output; 2: verbose output

*** These parameters are used for multi-loci partitioned data (ndata > 1), see dos Reis et al.(2013)

```

--------------------------------

### Find Best Partition Model Only (PartitionFinder Equivalent)

Source: https://github.com/iqtree/iqtree3/wiki/Advanced-Tutorial

Find the best partition model efficiently, mimicking PartitionFinder's approach. For IQ-TREE version 1.x, use -spp instead of -p.

```bash
iqtree -s example.phy -p example.nex -m TESTMERGEONLY
    # for version 1.x change -p to -spp
```

--------------------------------

### Symmetry Test Results Format

Source: https://github.com/iqtree/iqtree3/wiki/Assessing-Phylogenetic-Assumptions

Example structure of the .symtest.csv file generated by IQ-TREE, detailing results from matched-pair tests of symmetry for alignment partitions.

```csv
# Matched-pair tests of symmetry
# This file can be read in MS Excel or in R with command:
#    dat=read.csv('example.nex.symtest.csv',comment.char='#')
# Columns are comma-separated with following meanings:
#    Name:    Partition name
#    SymSig:  Number of significant sequence pairs by test of symmetry
#    SymNon:  Number of non-significant sequence pairs by test of symmetry
#    SymPval: P-value for maximum test of symmetry
#    MarSig:  Number of significant sequence pairs by test of marginal symmetry
#    MarNon:  Number of non-significant sequence pairs by test of marginal symmetry
#    MarPval: P-value for maximum test of marginal symmetry
#    IntSig:  Number of significant sequence pairs by test of internal symmetry
#    IntNon:  Number of non-significant sequence pairs by test of internal symmetry

```

--------------------------------

### Configure zlib.pc and zconf.h

Source: https://github.com/iqtree/iqtree3/blob/master/zlib-1.2.7/CMakeLists.txt

Configures the 'zlib.pc' pkgconfig file and the 'zconf.h' header file using CMake's configure_file command with '@ONLY' variable substitution.

```cmake
set(ZLIB_PC ${CMAKE_CURRENT_BINARY_DIR}/zlib.pc)
configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/zlib.pc.cmakein
		${ZLIB_PC} @ONLY)
configure_file( 	${CMAKE_CURRENT_SOURCE_DIR}/zconf.h.cmakein
		${CMAKE_CURRENT_BINARY_DIR}/zconf.h @ONLY)
```

--------------------------------

### Run UFBoot with IQ-TREE

Source: https://github.com/iqtree/iqtree3/wiki/Tutorial

Use the -B option to specify the number of bootstrap replicates for UFBoot. 1000 is the minimum recommended number. For IQ-TREE version 1.x, use -bb instead of -B.

```bash
iqtree -s example.phy -m TIM2+I+G -B 1000
    # for version 1.x change -B to -bb
```

--------------------------------

### Combining ECMK07 and GY2K Models

Source: https://github.com/iqtree/iqtree3/wiki/Substitution-Models

Example of a combined empirical-mechanistic codon model where rate entries are a multiplication of corresponding rate matrices from ECMK07 and GY2K models.

```text
ECMK07_GY2K
```

--------------------------------

### Find Best Partition Scheme, Tree Inference, and Bootstrap

Source: https://github.com/iqtree/iqtree3/wiki/Quickstart

Find the best partition scheme, followed by tree inference and ultrafast bootstrap with 1000 replicates. For version 1.x, change -B to -bb.

```bash
iqtree -s example.phy -p example.nex -m MFP+MERGE -B 1000
# for version 1.x change -B to -bb
```

--------------------------------

### Specify Empirical Amino-Acid Frequencies

Source: https://github.com/iqtree/iqtree3/wiki/Substitution-Models

Use the +F option to specify empirical amino-acid frequencies from the data. This example shows how to provide a custom list of frequencies.

```bash
+F{0.079066,0.055941,0.041977,0.053052,0.012937,0.040767,0.071586,0.057337,0.022355,0.062157,0.099081,0.064600,0.022951,0.042302,0.044040,0.061197,0.053287,0.012066,0.034155,0.069147}
```

--------------------------------

### Increase maximum categories for model testing

Source: https://github.com/iqtree/iqtree3/wiki/Tutorial

Increase the maximum number of categories tested for models, useful for longer sequence alignments. This example tests up to +R15.

```bash
iqtree -s example.phy -m MF -cmax 15
```

--------------------------------

### NEXUS Partition File with Non-Consecutive Sites

Source: https://github.com/iqtree/iqtree3/wiki/Advanced-Tutorial

Example of a NEXUS partition file defining a character set with non-consecutive sites, useful for extracting codon positions.

```nexus
#nexus
begin sets;
    charset part1 = 1-100 200-384;
    charset part1 = 1-100\3;
end;
```

--------------------------------

### Estimate Linked Exchangeabilities

Source: https://github.com/iqtree/iqtree3/wiki/Command-Reference

Use this command to estimate linked exchangeabilities for a protein alignment under a specified model and guide tree, initializing optimization from existing exchangeabilities.

```bash
iqtree -s prot.phy -m GTR20+C60+G --link-exchange --init-exchange LG -te guide.treefile
```

--------------------------------

### Infer ML Tree with Partition Model and Ultrafast Bootstrap

Source: https://github.com/iqtree/iqtree3/wiki/Command-Reference

Reconstruct an ML tree and perform ultrafast bootstrap (5000 replicates) using a partition model file.

```bash
iqtree -s data.phy -spp partition.nex -m TEST -bb 5000
```

--------------------------------

### Constrained Tree Search with IQ-TREE

Source: https://github.com/iqtree/iqtree3/wiki/Advanced-Tutorial

Applies a constraint to guide the tree search. Use `--prefix` (or `-pre` for v1.x) to specify an output file prefix.

```bash
iqtree -s example.phy -m TIM2+I+G -g example.constr1 --prefix example.constr1
# for version 1.x change --prefix to -pre
```

--------------------------------

### Specify OpenMP paths for macOS compilation

Source: https://github.com/iqtree/iqtree3/wiki/Compilation-Guide

If OpenMP include or library files are not found, set these environment variables before running CMake. Adjust the paths to your OpenMP installation.

```bash
export LDFLAGS="-L/opt/homebrew/opt/libomp/lib"
export CPPFLAGS="-I/opt/homebrew/opt/libomp/include"
cmake -DCMAKE_CXX_FLAGS="$LDFLAGS $CPPFLAGS" -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ ..
```

--------------------------------

### Basic IQ-TREE Invocation

Source: https://github.com/iqtree/iqtree3/wiki/Command-Reference

This is the fundamental command structure for running IQ-TREE. Replace `<alignment>` with the path to your sequence alignment file. Options can be appended as needed.

```bash
iqtree -s <alignment> [OPTIONS]
```

--------------------------------

### Simulating DNA Alignment with Jukes-Cantor Model

Source: https://github.com/iqtree/iqtree3/wiki/AliSim

Example of simulating a DNA alignment using the Jukes-Cantor model and a provided Newick tree file. The output is saved to 'alignment.phy'.

```bash
iqtree3 --alisim alignment -m "JC" -t tree.nwk
```