Downloading the data

The authors of the paper made data publicly available in a clean manner in this data repository.

We will download the Wheat_Relative_History_Data_Glemin_et_al.zip and move it into our data subfolder.

The authors uploaded the alignments, rather than raw data for us to assemble and align.

[discussion on alignment/assembly based on paper]

[final assessment of data at hand]

Installing required software

Software Note on Windows

For Windows users, some software is only available on Linux/Mac or has different installation instructions for Windows users. Fortunately Windows 11 (and more recent versions of Windows 10) can create a Linux-like environment relatively easily using the Windows Subsystem for Linux. Detailed installation instructions can be found here or from the command line you can run:

wsl --install

Now, from the command prompt you can enter wsl and you should enter a Linux environment where you can effectively install and use software that requires a Linux operating system. From here you should be able to use any software that only has a Linux/Mac installation instructions. It is important to note that like with any operating system, the programs need to be accessible from the command line. An easy way to do this is to ensure your software is located somewhere in your PATH. You can check the folders that are a part of your path with echo $PATH.

1. RAxML Next Generation

The repository for RAxML has installation instructions here.

For Mac

I click on Download OSX/macOS binary (x86 and ARM) and I download raxml-ng_v1.2.2_macos.zip. I put this folder in my computer (I have a folder software), and inside it is the executable raxml-ng.

I will copy this executable into /usr/local/bin so that I can call it from wherever in my machine, but you can also use the whole path.

cd software/raxml-ng_v1.2.2_macos/ ## you need to modify to your own path
ls ## check the raxml-ng executable is there
cp raxml-ng /usr/local/bin

When you try to run raxml-ng, your computer will complain that it cannot verify it is free of malware. You need to go to System Settings > Privacy and Security. Find the app and choose “Open Anyway”. Note that if you copied your executable on your PATH, you will need to choose “open anyway” twice: once for the file in the original path and once for when you call it somewhere else in your machine.

Confirm that you can run RAxML by typing raxml-ng in the terminal.

For Windows

This will need to be built in the Windows Subsystem for Linux. First, download the Linux binary for (RAxML-ng)[https://github.com/amkozlov/raxml-ng/releases/download/1.2.2/raxml-ng_v1.2.2_linux_x86_64.zip]. Extract the contents from this folder and you will find an executable file named raxml-ng, either add the location of raxml-ng to your PATH or move the file to a location already in your PATH. Now from the WSL, you can confirm you have installed RAxML with the command raxml-ng -h.

2. bppSuite (skipped)

The software repository has instructions for installation here.

Before git cloning bppsuite, we need to make sure we have installed specific libraries.

For Mac

Following this, we do:

brew tap jydu/homebrew-biopp
brew update ## optional
brew install libbpp-core libbpp-seq libbpp-phyl libbpp-popgen

Note that I had to update my OS and XCode.

Note that the libraries names change per Homebrew notation.

These are the project or library names:

bpp-core
bpp-seq
bpp-phyl
bpp-popgen

Homebrew prefixes most C/C++ libraries with lib to make it explicit that they install libraries, hence:

libbpp-core
libbpp-seq
libbpp-phyl
libbpp-popgen

I get the following error due to cmake version:

$ brew install libbpp-core libbpp-seq libbpp-phyl libbpp-popgen
==> Fetching downloads for: libbpp-core, libbpp-seq, libbpp-phyl and libbpp-popgen
✔︎ Bottle Manifest cmake (4.2.1)                           [Downloaded   11.4KB/ 11.4KB]
✔︎ Bottle cmake (4.2.1)                                    [Downloaded   20.1MB/ 20.1MB]
✔︎ Formula libbpp-core (2.4.1)                             [Verified    361.3KB/361.3KB]
✔︎ Formula libbpp-seq (2.4.1)                              [Verified    322.6KB/322.6KB]
✔︎ Formula libbpp-phyl (2.4.1)                             [Verified    600.4KB/600.4KB]
✔︎ Formula libbpp-popgen (2.4.1)                           [Verified    116.9KB/116.9KB]
==> Installing libbpp-core from jydu/biopp
==> Installing jydu/biopp/libbpp-core dependency: cmake
==> Pouring cmake--4.2.1.sequoia.bottle.tar.gz
🍺  /usr/local/Cellar/cmake/4.2.1: 4,016 files, 66.8MB
==> cmake ..
Last 15 lines from /Users/Clauberry/Library/Logs/Homebrew/libbpp-core/01.cmake.log:
-Wno-dev
-DBUILD_TESTING=OFF
-DCMAKE_OSX_SYSROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX15.sdk

CMake Error at CMakeLists.txt:8 (cmake_minimum_required):
  Compatibility with CMake < 3.5 has been removed from CMake.

  Update the VERSION argument <min> value.  Or, use the <min>...<max> syntax
  to tell CMake that the project requires at least <min> but has been updated
  to work with policies introduced by <max> or earlier.

  Or, add -DCMAKE_POLICY_VERSION_MINIMUM=3.5 to try configuring anyway.


-- Configuring incomplete, errors occurred!

If reporting this issue please do so at (not Homebrew/* repositories):
  https://github.com/jydu/homebrew-biopp/issues

I asked ChatGPT, and they suggest forcing the cmake version:

export CMAKE_POLICY_VERSION_MINIMUM=3.5
brew install libbpp-core

brew install libbpp-core \
  --cmake-args="-DCMAKE_POLICY_VERSION_MINIMUM=3.5"

But neither works!

From the paper, it seems they only use bppSuite for re-rooting the gene trees: “BppReroot of the BppSuite (42, 43) was used to reroot the 13,288 gene trees, using as outgroups the following ordered list of species: H_vulgare, Er_bonaepartis, S_vavilovii, and Ta_caputMedusae.”

So, we will skip this software for now.

3. SSIMUL

We download the binaries from the software website for Mac and Linux here.

The zipped folder ssimul.zip contains the executables.

Note for Windows users: We will use again the Windows Subsystem for Linux.

4. SuperTriplets

SuperTriplets comes packaged as a Java program and thus requires Java. You can check if you have Java installed on your machine with the command java -h. If Java is not installed, you can download it here.

Note for Windows users: unless you explicitly download Java in the WSL, you will only be able to use Java programs outside your WSL (i.e., in the normal command prompt before typing wsl).

There is download information in the SuperTriplets website.

You simply download the java file SuperTriplets_v1.1.jar. I put it in my computer software folder inside a subfolder named supertriplets. We will have to use the whole path when calling this function:

java -jar -Xmx500m ~/software/supertriplets/SuperTriplets_v1.1.jar newick_file.nwk outfile

5. ASTRAL

The ASTRAL repo recommends us to use the new C code ASTER. Installation instructions are within.

For Mac

For me, installing with conda worked:

conda install aster

To know where everything was installed:

$ which wastral
/Users/Clauberry/.julia/conda/3/bin/wastral

And you can test it works by:

$ wastral

For Windows

You can download the binary from here. All of the various forms of ASTRAL are included in the exe/ folder and you should make sure these files are a part of your PATH. You can confirm correct installation by running waster -h.

Alternatively, if you need to install from source, you can build in WSL and installation instructions can be found here.

6. Julia and packages

I recommend installing Julia via JuliaUp as this allows you to have multiple Julia versions installed.

For Mac

Install JuliaUp:

curl -fsSL https://install.julialang.org | sh

Install Julia:

juliaup add release

For Windows

Julia can be installed by following the directions here or directly from the Julia website Windows app store.

Once Julia is Installed

Start Julia by typing julia in the terminal. Inside Julia, install packages by first pressing ] to go into package mode (the prompt will change to (@v1.12) pkg>):

add PhyloNetworks
add SNaQ
add PhyloPlots

Leave Julia by typing exit().

7. HyDe

We will follow the installation commands from the github repo.

HyDe requires Python. You can install the latest version of Python for your machine here. You can check installation by running the command python -h or pythonX.XX -h where X.XX is the version number of python.

The files can be downloaded with:

git clone https://github.com/pblischak/HyDe.git

Next move into the HyDe folder and install HyDe:

cd HyDe
python3.11 -m pip install -r requirements.txt
python3.11 -m pip install .

Note for Mac users that I had updated XCode, but did not agree to the new license, so I was getting weird errors because of that.

Note for Windows users: You will need a the Microsoft Visual C++ compiler that is at least version 14.0; that can be downloaded here. When going thru the installer, select “Desktop Development with C++”. Alternatively, if you downloaded Python for the WSL and want HyDe on the WSL, you can follow the download instructions using any C++ compiler.

You can confirm installation by running make test.

8. R

Those that don’t have them should install R and RStudio, see here.

Inside R:

install.packages("ape")
install.packages("phangorn")
install.packages("BiocManager")
BiocManager::install("YuLab-SMU/treedataverse")
install.packages("MSCquartets")
install.packages("phytools")