Selecting a Workflow

1. Choose a Workflow

   1. Placement workflow (Fast): Automatically places uploaded genomes into a pruned GTDB-based reference tree using Mash distance. Suitable for quick, high-level placements.
   2. De novo workflow (Accurate): Allows custom tree construction using selected organisms and genes. Suitable for in-depth phylogenetic analysis.

2. Upload genome file(s) in FASTA or GenBank each containing one organism.
3. Optional: provide an email for job updates, a title, or save the job to your browser (via cookies).

2. Upload up to 50 genome files. Same format requirements as above.
3. Choose tree type:
   • Concatenated: Concatenated Phylogeny, using concatenated matrix.
   • Coalescent: Default MLST tree, based on gene tree consensus.
4. Optional parameters:
   • Enable automatic species/gene selection.
   • Enable bootstrapping (Ultrafast Bootstrap).
   • Enable ModelFinder for best-fit models.
5. Optional job parameters (email, title, cookie storage).

6. Edit default selection of 50 closest genomes. Exceeding selections are ignored.
7. Filter, search, and explore metadata for selected and additional species.
8. Optionally select your desired outgroup genome.

1. ANI table shows closest matches by Mash distance. Search and sort functions available.

Tree types and options vary by workflow. Tree nodes are color-coded (QS = blue, OG = red, TS = green).

1. Toggle between scaled and unscaled branch display.
2. Search and highlight organisms in the tree.
3. Display options include:
   1. Highlighting BGC potential
   2. Strain info highlighting
   3. Highlighting a specific BGC group
4. Additional data about reference genomes
5. Downloads:
   • Newick tree (no color)
   • SVG tree image
   • Alignment files (ZIP) (denovo only)
   • Gene list (denovo only)
   • ANI table (full)