git clone
cd clustrace
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 | |||
| MAFFT v7 | biokit | |||
| MsaToVcf | NA | NA | ||
| Pangolin | bioconda | NA | ||
| SeqKit | NA | |||
| snpEff | NA | NA | ||
| TreeCluster | NA | NA | ||
| Trimal | biokit | |||
| VeryFastTree | NA | NA | ||
| PERL MODULES | ||||
| biokit | ||||
| NA |
Table1: ClusTRace dependencies
For more information please see