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| <h1 id="parallelevolccm-usage">ParallelEvolCCM usage</h1> | ||
| <p>ParallelEvolCCM is a tool for the identification of coordinated gain and loss of features. | ||
| The method is described in detail in the following publication:</p> | ||
| <ul> | ||
| <li><a href="https://doi.org/10.1093/sysbio/syac052">The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles</a></li> | ||
| </ul> | ||
| <p>If you use ParallelEvolCCM in your analysis, please cite the above publication.</p> | ||
| <h2 id="parallelevolccm-inputs">ParallelEvolCCM inputs</h2> | ||
| <p>The ParallelEvolCCM tool requires two inputs:</p> | ||
| <ul> | ||
| <li>A phylogenetic tree in Newick format</li> | ||
| <li>A presence/absence table in TSV format.</li> | ||
| </ul> | ||
| <p>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.:</p> | ||
| <pre><code>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 | ||
| </code></pre> | ||
| <h2 id="using-parallelevolccm-by-itself">Using ParallelEvolCCM by itself</h2> | ||
| <p>The ParallelEvolCCM tool is a command line tool written in R. | ||
| It is available through the <a href="https://github.com/beiko-lab/arete/blob/master/bin/ParallelEvolCCM.R">bin/ParallelEvolCCM.R</a> script.</p> | ||
| <p>To download the tool and make it executable, run:</p> | ||
| <pre><code class="language-bash">wget https://raw.githubusercontent.com/beiko-lab/arete/master/bin/ParallelEvolCCM.R | ||
| chmod +x ParallelEvolCCM.R | ||
| </code></pre> | ||
| <p>Then, ensure all EvolCCM dependencies are installed. | ||
| You can install them by running the following command in your R console:</p> | ||
| <pre><code class="language-r">install.packages(c('ape', 'dplyr', 'phytools', 'foreach', 'doParallel', 'gplots', 'remotes')) | ||
| remotes::install_github('beiko-lab/evolCCM') | ||
| </code></pre> | ||
| <p>You can then run the tool like this:</p> | ||
| <pre><code class="language-bash">./ParallelEvolCCM.R --intree tree.nwk --intable feature_table.tsv.gz --cores -1 | ||
| </code></pre> | ||
| <ul> | ||
| <li><code>--intree</code> specifies the phylogenetic tree in Newick format.</li> | ||
| <li><code>--intable</code> specifies the feature table in compressed TSV format.</li> | ||
| <li><code>--cores</code> specifies the number of cores to use. Use <code>-1</code> to use all available cores.</li> | ||
| </ul> | ||
| <p>Additional parameters can be found by running <code>./ParallelEvolCCM.R</code> with no additional parameters.</p> | ||
| <h2 id="using-parallelevolccm-with-arete">Using ParallelEvolCCM with ARETE</h2> | ||
| <p>The ParallelEvolCCM tool is also made available through the <code>evolccm</code> entry in ARETE. | ||
| Making it possible to run the tool with Docker or Singularity.</p> | ||
| <p>To execute the ParallelEvolCCM tool with ARETE, run the following command:</p> | ||
| <pre><code class="language-bash">nextflow run beiko-lab/ARETE \ | ||
| -entry evolccm \ | ||
| --core_gene_tree core_gene_alignment.tre \ | ||
| --feature_profile feature_profile.tsv.gz \ | ||
| -profile docker | ||
| </code></pre> | ||
| <p>The parameters being:</p> | ||
| <ul> | ||
| <li><code>--core_gene_tree</code> - The reference tree, coming from a core genome alignment, | ||
| like the one generated by the <code>phylo</code> entry in ARETE.</li> | ||
| <li><code>--feature_profile</code> - A presence/absence TSV matrix of features | ||
| in genomes, like the one created in ARETE's <code>annotation</code> entry.</li> | ||
| <li><code>-profile</code> - The profile to use. In this case, <code>docker</code>.</li> | ||
| </ul> | ||
| <p>For more information, check the <a href="https://beiko-lab.github.io/arete/">full ARETE documentation</a>.</p> | ||
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