+
+ +

ParallelEvolCCM usage

+

ParallelEvolCCM is a tool for the identification of coordinated gain and loss of features. +The method is described in detail in the following publication:

+ +

If you use ParallelEvolCCM in your analysis, please cite the above publication.

+

ParallelEvolCCM inputs

+

The ParallelEvolCCM tool requires two inputs:

+
    +
  • A phylogenetic tree in Newick format
    • +
  • A presence/absence table in TSV format.
    • +
+

The presence/absence TSV must have genome names equal to the ones in the tree in a 'genome_id' column, +with all other columns representing features absent (0) or present (1) in each genome. I.e.:

+
genome_id   plasmid_AA155   plasmid_AA161
+ED010   0   0
+ED017   0   1
+ED040   0   0
+ED073   0   1
+ED075   1   1
+ED082   0   1
+ED142   0   1
+ED178   0   1
+ED180   0   0
+
+

Using ParallelEvolCCM by itself

+

The ParallelEvolCCM tool is a command line tool written in R. +It is available through the bin/ParallelEvolCCM.R script.

+

To download the tool and make it executable, run:

+
wget https://raw.githubusercontent.com/beiko-lab/arete/master/bin/ParallelEvolCCM.R
+chmod +x ParallelEvolCCM.R
+
+

Then, ensure all EvolCCM dependencies are installed. +You can install them by running the following command in your R console:

+
install.packages(c('ape', 'dplyr', 'phytools', 'foreach', 'doParallel', 'gplots', 'remotes'))
+remotes::install_github('beiko-lab/evolCCM')
+
+

You can then run the tool like this:

+
./ParallelEvolCCM.R --intree tree.nwk --intable feature_table.tsv.gz --cores -1
+
+
    +
  • --intree specifies the phylogenetic tree in Newick format.
    • +
  • --intable specifies the feature table in compressed TSV format.
    • +
  • --cores specifies the number of cores to use. Use -1 to use all available cores.
    • +
+

Additional parameters can be found by running ./ParallelEvolCCM.R with no additional parameters.

+

Using ParallelEvolCCM with ARETE

+

The ParallelEvolCCM tool is also made available through the evolccm entry in ARETE. +Making it possible to run the tool with Docker or Singularity.

+

To execute the ParallelEvolCCM tool with ARETE, run the following command:

+
nextflow run beiko-lab/ARETE \
+  -entry evolccm \
+  --core_gene_tree core_gene_alignment.tre \
+  --feature_profile feature_profile.tsv.gz \
+  -profile docker
+
+

The parameters being:

+
    +
  • --core_gene_tree - The reference tree, coming from a core genome alignment, + like the one generated by the phylo entry in ARETE.
    • +
  • --feature_profile - A presence/absence TSV matrix of features + in genomes, like the one created in ARETE's annotation entry.
    • +
  • -profile - The profile to use. In this case, docker.
    • +
+

For more information, check the full ARETE documentation.

+ +
+