Installing ClusTRace

Clone the repository

git clone https://plyusnin@bitbucket.org/plyusnin/clustrace.git
cd clustrace

Install Bioinformatic tools

Install binaries with Conda

conda create -n clustrace -c bioconda iqtree mafft jvarkit-msa2vcf pangolin seqkit snpeff treecluster trimal veryfasttree
conda activate clustrace

Or install from yaml file

conda env create -f clustrace.env.yml
conda activate clustrace

Install Perl Modules

Install perl modules to ~/perl5 (or choose another directory according to your settings):

cpanm --local-lib=~/perl5 Clone Excel::Writer::XLSX File::Temp Getopt::Long Sort::Naturally Struct::Dumb Time::Piece
# install BioPerl
cpanm -i -f --notest --local-lib=~/perl5 Bio::TreeIO
#add this line to your ~/.bashrc file
export PERL5LIB=~/perl5/lib/perl5

Complete list of dependencies

Tool CSC module Website Direct download Original article
IQ-TREE 2 NA http://www.iqtree.org/ linux 64-bit https://doi.org/10.1093/molbev/msaa015
MAFFT v7 biokit https://mafft.cbrc.jp/alignment/software/ linux 64-bit https://doi.org/10.1093/molbev/mst010
MsaToVcf NA http://lindenb.github.io/jvarkit/MsaToVcf.html NA https://doi.org/10.1099/mgen.0.000056
Pangolin bioconda https://cov-lineages.org/resources/pangolin.html NA https://doi.org/10.1093/ve/veab064
SeqKit NA https://bioinf.shenwei.me/seqkit/ linux 64-bit https://doi.org/10.1371/journal.pone.0163962
snpEff NA http://pcingola.github.io/SnpEff/ NA https://doi.org/10.4161/fly.19695
TreeCluster NA https://github.com/niemasd/TreeCluster NA https://doi.org/10.1371/journal.pone.0221068
Trimal biokit http://trimal.cgenomics.org/ linux 64-bit https://doi.org/10.1093/bioinformatics/btp348
VeryFastTree NA https://github.com/citiususc/veryfasttree NA https://doi.org/10.1093/bioinformatics/btaa582
PERL MODULES        
  biokit Bio::TreeIO    
  NA Excel::Writer::XLSX File::Temp Getopt::Long Sort::Naturally Struct::Dumb Time::Piece    

Table1: ClusTRace dependencies

For more information please see https://bitbucket.org/plyusnin/clustrace/src/master/