Help

Quick start

1. On the submit page, choose a nucleotide FASTA file.
2. Pick a gene predictor (PHANOTATE is the phage-optimised default) and, if you like, leave fast mode on.
3. Submit. You'll be taken straight to a status page you can bookmark or share -- it updates itself as pharokka, phold and phynteny each finish.

Input requirements

• Plain nucleotide FASTA, or gzip/bzip2/zstd-compressed.
• Up to 20 contigs per submission.
• Each contig between 100 and 2,000,000 bp.
• Up to 2,000,000 bp total across all contigs.
• Upload size up to 50 MB on the wire (200 MB decompressed).
• Standard IUPAC nucleotide codes only -- protein FASTA is detected and rejected with a specific message.

This is a single-genome / small-multi-contig service, not a metagenome pipeline. If you have a large metagenomic assembly, running the tools locally is a better fit -- see each tool's own repository for installation instructions.

Gene predictors

PHANOTATE (default -- phage-optimised gene caller)

A gene-calling model trained specifically on phage genomes. The default, and usually the best choice.

Prodigal

A general-purpose bacterial/archaeal gene predictor.

Prodigal-GV (for jumbo phages / giant viruses)

A Prodigal variant tuned for giant viruses and other unusual genomic contexts.

Reading the status page

The three-stage tracker shows which of pharokka, phold and phynteny is currently running. The stages run strictly in that order -- phold consumes pharokka's output, and phynteny consumes phold's -- so there's no parallel fan-out to speed up by re-submitting.

Reading the results page

Results are organised into one tab per stage. The Phynteny tab is shown by default, since its output is the most complete: everything phold found, plus predictions for the genes that were still unknown after phold. Each tab's table is sortable (click a column header) and filterable (type in the box above it), and every file shown is downloadable individually, or all together as a single zip.

Common rejection reasons

"Zip and other multi-file archives aren't supported"

Upload a single FASTA file, optionally gzip/bzip2/zstd-compressed -- not a .zip containing one.

"This looks like a protein sequence"

The pipeline needs the nucleotide genome, not a translated protein FASTA.

"The file has more contigs than the public tier allows"

This service targets single genomes / small multi-contig assemblies, capped at 20 contigs -- see above.

"Two or more contigs share the same identifier"

Every contig header in the file needs a unique ID.

Finding your jobs again

Every submission gets a shareable status link (/jobs/<id>) -- bookmark it or save it somewhere, since that link is the durable way to get back to a result. This browser also remembers jobs you've submitted from it under My jobs, purely as a convenience (it's local to this browser only, and lost if you clear site data).

See About for data retention and privacy, and How to cite for citation information.