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Phylogenetic Trees

Arx can generate and display phylogenetic trees using three distinct algorithms:

  • TaxId-based tree: Short calculation time but based on taxid-annotations only (NOT on sequence similarity).
  • Genome-similarity-based tree: Short calculation time, based on pairwise comparisons of assemblies (default: GenDisCal (preset approxANI, see footnotes) (Goussarov et al., Bioinformatics, 2020)
  • Single-copy-ortholog-based tree (core-genome-based tree): Long calculation time. The methodology is based on OrthoFinder consensus tree of all single-copy ortholog alignments (Emms et al., Genome Biology, 2019)

trees demo

How to get there

In the genome table, select multiple genomes (using Shift and Ctrl) and open the context menu using right click. Then, click on Show phylogenetic trees.

Background processing

Tree and ANI computations run as background jobs. After submitting, you can close the tab or navigate elsewhere; the calculation continues on the server. Results are saved and can be reopened from the Job Queues page at any time.

ANI dendrogram

In addition to the heatmap view, pairwise ANI results include a dendrogram. Switch between views using the tabs above the result panel.

Uploading a tree

A Newick-format tree can be uploaded directly on the trees page instead of computing one from genomes. This is useful when you already have a tree from an external tool and want to visualize it alongside Arx genome metadata.

Advanced usage

Through the settings sidebar, it is possible to apply custom colors to the genomes in the tree.

Copy the newick string to use the dendrogram in external tools (e.g. phylo.io or iTOL).

Additional downloads:

  • For genome-similarity-based trees, download the distance matrix by clicking Download distance matrix or Copy distance matrix.
  • For single-copy-ortholog-based trees, download the full OrthoFinder output by clicking Download as .tar.xz. If this option is not available, click Reload OrthoFinder to regenerate the file.

Footnotes

GenDisCal, preset approxANI

The distance matrix is based on whole genome nucleotide similarity calculated using GenDisCal (Goussarov et al., Bioinformatics, 2020) with the approxANI preset. This preset is documented as follows:

approxANI is a minhash-based approximation of Average Nucleotide Identity (ANI). This method is similar to the one used by the Mash software (Ondov et al., Gen. biol., 2016) The ambiguity region for species is [0.04-0.06]

Thus, the GenDisCal similarities should produce values that strongly correlate with original ANI, but can be computed much faster.