PhaBOX 2.1.1

Updates:

• Integrate the PhaVIP into phabox2, and provide more detailed protein annotations. In this version, phavip will be automatically called when running end_to_end, phamer, phatyp, phagcn, and cherry. The outputs are named gene_annotation.tsv in the xxx_supplementary folder.
• End_to_end/PhaMer will provide an additional file named uncertain_sequences_for_contamination_task.fa and the outputs in the phamer_prediction.tsv will suggest the user run the contamination task to check the quality of these sequences (probability proviruses or novel viruses.
• CHERRY will provide a full lineage for the host in either the NCBI or GTDB version. However, because CHERRY is based on sequences from NCBI for prediction, some of them cannot find the corresponding lineage in GTDB.
• CHERRY will assign a score of 0 for the unpredicted host now rather than 'nan'.
• Fixed an issue where PhaTYP might not output anything when there was no alignment result for the input sequence.
• Fixed a possible problem when the length of the input sequence is equal to the filtering threshold.
• Revised some typos in the help documents.

PhaBOX 2.1.0

New updates:

1. Fix some bugs in the v2.0 version
2. Add bacterial MAGs version in Host prediction (Cherry)
3. Add vOTU grouping module
4. Add marker-searching module for the phylogenetic tree

The functions available currently:

🎉 Generalize for all kinds of viruses with faster speed! But we will call it PhaBOX2, not VirBOX, for a better inheritance ：)

🎉 Provide a more comprehensive taxonomy classification (latest ICTV 2024) and complete taxonomy lineage

🎉 Provide a genus-level clustering for potential new genera (genus-level vOTU)!

🎉 Provide a protein annotation function!

🎉 Provide a contamination and prophage detection module!

🎉 Allowing to predict host using bacterial MAGs

🎉 Provide a vOTU grouping module

🎉 Provide a marker-searching module for the phylogenetic tree

🎉 More user-friendly commands!

PhaBOX 1.0

The release for PhaBOX 1.0 version

including all the original scripts, database, parameters, and a README file