PhaBOX 2.1.7

Nov 27th, 2024

Important

Adjust the default parameters for the phylogenetic task
- marker alignment coverage --mcov: 50
- marker alignment identity --mpident: 25

• Add message information when the calling program (diamond, blast+, fasttree, etc.) fails.

PhaBOX 2.1.6

Nov 21th, 2024

• Revised some typos in the --help descriptions
• Host nodes are added to the cherry's network for better visualization

PhaBOX 2.1.5

Nov 6th, 2024

Version 2.1.4

Updates:

• Fixed a bug that --task tree will incorrectly combine DNA and Protein sequences in one file
• Fixed some typos in the scripts

PhaBOX 2.1.4

Nov 6th, 2024

Version 2.1.4

Updates:

• All the os.system() are replaced by subprocess.run(), providing standard error and return a non-zero exit code in case one of the calls fails.
• Providing a short parameters for --dbdir (-d) and --outpth (-o)

PhaBOX 2.1.3

Nov 4th, 2024

Version 2.1.3

Updates:

• PhaVIP will provide an additional output phavip_prediction.csv. A detailed explanation of this file can be found via PhaVIP outputs
• The protein annotation file gene_annotation.tsv will provide the alignment identity and coverage information as new columns.
• Fixed a potential issue when running phylogenetic tree (FastTree) in the tree task. Users should re-download the PhaBOX v2 database if they would like to run the tree task. Download link
• Fixed a typo in the PhaTYP program.

PhaBOX 2.1.2

Updates:

• End_to_end mode will only make predictions on the predicted viruses. For low-confidence viruses and non-viruses with a flag lower than the viral score threshold, we provide a file named uncertain_sequences_for_contamination_task.fa. We suggest the user run the contamination task to check the quality of their sequences first.
• The contamination task will provide four more fasta files for users: low_quality_virus.fa, medium_quality_virus.fa, high_quality_virus.fa and a cropped proviruses.fa. Users can use them to re-run other tasks.

PhaBOX 2

PhaBOX has now been upgraded to the 2.0 version with faster speed!

There are some major components, including:

🎉 Generalized to all kinds of viruses

🎉 Virus identification

🎉 Taxonomy classification

🎉 Host prediction

🎉 Lifestyle prediction

🎉 Contamination/provirus detection

🎉 vOTU grouping

🎉 Phylogenetic tree based on marker genes

🎉 Viral protein annotation

🎉 All the databases are updated to the latest ICTV 2024 release

If you have any more suggestions, feel free to let me know! We consider long-term maintenance PhaBOX and adding modules according to your needs

You can post an issue or directly email me ([email protected]). We welcome any suggestions.

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