This guide provides detailed instructions how to set up ClusTRace on Puhti server (CSC). Installing on other unix serveres follows similar steps.

Start by cloning the repository

git clone

Install bioinformatic tools

Tool CSC module Website Direct download Original article
IQ-TREE 2 NA linux 64-bit
MAFFT v7 biokit linux 64-bit
MsaToVcf NA NA
Pangolin bioconda NA
SeqKit NA linux 64-bit
snpEff NA NA
TreeCluster NA NA
Trimal biokit linux 64-bit
VeryFastTree NA NA

Hint: you do not need to install all tools, just those that you intend to use (e.g. IQ-Tree2 or VeryFastTree).

Install Perl Modules

module load biokit # run on CSC to load correct Perl env
cpanm --local-lib=~/perl5 Bio::SeqIO Bio::TreeIO Clone Excel::Writer::XLSX File::Basename File::Temp Getopt::Long Sort::Naturally Struct::Dumb Time::Piece
#add this line to your ~/.bashrc file
export PERL5LIB=~/perl5/lib/perl5

For more information please see