Linux software installation

These are instructions for how to install software and data used on the course Computational Molecular Evolution (22115) when using the Linux operating system.

The commands assume you are using the apt package manager used on e.g. Ubuntu Linux.

Note: If your computer uses a CPU based on the ARM architecture, rather than the more common Intel or AMD (x86_64) architectures, some commands may need to be adjusted. Please let me know if this applies to you, so I can provide additional instructions tailored for ARM-based systems

# Use the out-commented commands below if you want to copy my premade .bashrc file for customising bash
# WARNING: do not owerwrite a pre-existing .bashrc unless you are sure it contains nothing you want to keep
# NOTE: if you are using a different shell, then you should use the corresponding .rc file (e.g., .zshrc for zsh)
# wget https://teaching.healthtech.dtu.dk/material/22115/bashrc.txt
# mv bashrc.txt ~/.bashrc

# Compiler, make, other system tools needed below
sudo apt-get install build-essential

# Java
sudo apt install openjdk-17-jre

# Nedit
# NOTE: you can use any plain-text editor you prefer
sudo apt update
sudo apt -y install nedit

# MrBayes
# Note: I am using the flag --disable-sse to avoid crashes on some machines
# It is possible that mb will run faster if you omit this flag
sudo apt -y install git
git clone --depth=1 https://github.com/NBISweden/MrBayes.git ~/MrBayes
cd ~/MrBayes
./configure --disable-sse
make
sudo make install
cd ..

# PAUP
# NOTE: the linux version of paup has some issues with being linked against older libraries
# I have tried a work-around below, but there may be issues
wget https://phylosolutions.com/paup-test/paup4a169_ubuntu64.gz
gunzip paup4a169_ubuntu64.gz
chmod 755 paup4a169_ubuntu64
sudo mv paup4a169_ubuntu64 /usr/local/bin/paup4a169 
mkdir -p ~/opt/paup-compat
wget https://archive.ubuntu.com/ubuntu/pool/universe/g/gcc-7/libgfortran4_7.5.0-6ubuntu2_amd64.deb
wget https://archive.ubuntu.com/ubuntu/pool/universe/p/python2.7/libpython2.7_2.7.18-1~20.04.7_amd64.deb
dpkg-deb -x libpython2.7_2.7.18-1~20.04.7_amd64.deb ~/opt/paup-compat
dpkg-deb -x libgfortran4_7.5.0-6ubuntu2_amd64.deb ~/opt/paup-compat
cat >> ~/.bashrc <<'EOF'

# PAUP* wrapper: add compat libs (libpython2.7, libgfortran4) at runtime
paup () {
  export LD_LIBRARY_PATH="$HOME/opt/paup-compat/usr/lib/x86_64-linux-gnu:${LD_LIBRARY_PATH:-}"
  /usr/local/bin/paup4a169 "$@"
}

EOF
rm libgfortran4_7.5.0-6ubuntu2_amd64.deb libpython2.7_2.7.18-1~20.04.7_amd64.deb

# IQ-TREE 3
wget https://github.com/iqtree/iqtree3/releases/download/v3.0.1/iqtree-3.0.1-Linux.tar.gz
sudo tar -xvf iqtree-3.0.1-Linux.tar.gz --directory /usr/local/src
echo "alias iqtree3='/usr/local/src/iqtree-3.0.1-Linux/bin/iqtree3'" >> ~/.bashrc

# PAML
sudo apt -y install paml

# jmodeltest
wget https://github.com/ddarriba/jmodeltest2/files/157117/jmodeltest-2.1.10.tar.gz
sudo tar -xvf jmodeltest-2.1.10.tar.gz --directory /usr/local/src
rm jmodeltest-2.1.10.tar.gz
echo "alias jmodeltest='java -jar /usr/local/src/jmodeltest-2.1.10/jModelTest.jar'" >> ~/.bashrc

# BEASTX
wget https://github.com/beast-dev/beast-mcmc/releases/download/v10.5.0/BEAST_X_v10.5.0.tgz
sudo tar -zxvf BEAST_X_v10.5.0.tgz --directory /usr/local/src
echo 'PATH="/usr/local/src/BEASTv10.5.0/bin${PATH:+:${PATH}}"' >> ~/.bashrc

# FigTree
sudo apt -y install figtree

# Tracer
wget https://github.com/beast-dev/tracer/releases/download/v1.7.2/Tracer_v1.7.2.tgz
sudo mkdir /usr/local/src/Tracer
sudo tar -zxf Tracer_v1.7.2.tgz --directory /usr/local/src/Tracer
sudo ln -s /usr/local/src/Tracer/bin/tracer /usr/local/bin/
rm Tracer_v1.7.2.tgz

# TempEst
wget --content-disposition 'https://tree.bio.ed.ac.uk/download.php?id=102&num=3'
sudo tar -zxf TempEst_v1.5.3.tgz --directory /usr/local/src/
sudo chmod 755 /usr/local/src/TempEst_v1.5.3/bin/tempest
sudo ln -s /usr/local/src/TempEst_v1.5.3/bin/tempest /usr/local/bin/
rm TempEst_v1.5.3.tgz

# MAFFT
sudo apt -y install mafft

# Aliview
wget https://ormbunkar.se/aliview/downloads/linux/linux-version-1.30/aliview.install.run
chmod 755 aliview.install.run
sudo ./aliview.install.run
rm aliview.install.run

# Anders Gorm software: sumt, seqconverter, phylotreelib
# https://github.com/agormp/phylotreelib
# https://github.com/agormp/sumt
# https://github.com/agormp/seqconverter
sudo apt-get install python3-pip
pip3 install seqconverter
pip3 install phylotreelib
pip3 install sumt
echo 'export PATH="$HOME/.local/bin:$PATH"' >> ~/.bashrc

# maxalign tool (see: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-312)
wget https://teaching.healthtech.dtu.dk/material/22115/maxalign.pl
chmod 755 maxalign.pl
sudo mv maxalign.pl /usr/local/bin

# R, Rstudio
# NOTE: Windows users may consider installing native Windows versions instead, and move files between file systems
sudo apt -y install r-base r-base-dev gdebi-core
wget https://download1.rstudio.org/electron/jammy/amd64/rstudio-2026.01.0-392-amd64.deb
sudo gdebi -n ./rstudio-2026.01.0-392-amd64.deb
rm rstudio-2026.01.0-392-amd64.deb

# Dependencies for R-packages
sudo apt -y install libcurl4-openssl-dev libxml2-dev libgit2-dev libopenblas-base

# Clean up
sudo apt autoremove --purge
sudo apt clean

# Activate changes to .bashrc in current shell
source ~/.bashrc

# Set up molevol directory for course exercises
# You can place this directory anywhere you prefer: 
# Just replace tilde (~) in the command below with path to preferred base directory
# (The tilde symbol is short for the user's home directory)
cd ~
mkdir molevol
wget https://teaching.healthtech.dtu.dk/material/22115/data.tar.gz
tar -xvf data.tar.gz --directory molevol
rm data.tar.gz

# R packages (do this inside Rstudio)
install.packages("tidyverse")
install.packages("bayesplot")