Taxid-based
Fastest

Based solely on taxid-annotations. Does not use sequence similarity. Best for quick overviews.

Genome-similarity
Fast

Uses pairwise comparisons of assemblies (GenDisCal / approxANI). A good balance of speed and accuracy.
Runs as a background job.

OrthoFinder-based
Slow

Most accurate phylogenetic tree. Uses consensus tree of single-copy ortholog alignments (core-genome).
Runs as a background job.

Tree display & colors (click to toggle)
Selected genomes will be highlighted across the currently visible tree.
Affects how branches are drawn.