Phage and virus biology · Software
BACPHLIP
Predicts whether a bacteriophage genome represents a temperate or virulent lifestyle using conserved protein domains.
What BACPHLIP is
BACPHLIP is a computational tool developed by Adam J. Hockenberry and Claus O. Wilke for predicting bacteriophage lifestyles directly from nucleotide sequence data. It determines whether an input phage genome follows a temperate (lysogenic) or virulent (lytic) infection cycle, addressing the challenge of lifestyle annotation in viral genomics.
Bacteriophage lifestyle classification is critical for understanding viral ecology, host-pathogen interactions, and selecting suitable candidates for phage therapy. BACPHLIP provides a standardised, automated approach to this prediction problem by identifying protein domains characteristically associated with temperate phages and processing them through a machine learning classifier.
How it works
The analysis begins with a complete bacteriophage nucleotide genome sequence in FASTA format. The pipeline translates the nucleotide sequence across all six reading frames and employs the external HMMER3 tool (specifically hmmsearch) to detect a curated panel of candidate temperate-specific protein domains.
The detected domain hits are processed and supplied to a trained random forest classifier. The model operates under the default assumption that the input phage is virulent; when a sufficient number and configuration of lysogeny-associated protein domains are identified, the classifier updates the prediction to temperate. It outputs the estimated probabilities of the genome belonging to the virulent or temperate class in a tab-separated format.
Key facts
- Software type
- Command-line tool and Python library
- Input format
- Nucleotide FASTA (.fasta) of complete phage genomes
- Output format
- Tab-separated values (.bacphlip)
- Model architecture
- Random forest classifier
- External dependencies
- HMMER3 (hmmsearch)
- Python dependencies
- Biopython, pandas, joblib, scikit-learn
- Training dataset composition
- Predominantly Caudovirales phages infecting Actinobacteria, Gammaproteobacteria, and Bacilli
What you can use it for
- Single-genome lifestyle classification
- Determining whether an individual newly sequenced bacteriophage genome is temperate or virulent using the command-line interface or Python API.
- Batch lifestyle screening of phage collections
- Processing multi-FASTA files containing multiple complete phage genomes to generate high-throughput tabular lifestyle predictions.
- Modular genome translation and domain searching
- Using individual Python library functions to execute six-frame translation, HMMER searches, and feature extraction as independent pipeline steps.
Run it here
Ask the research agent and it runs BACPHLIP as a job on a dedicated machine, then reads the results back to you. Nothing to install, and it keeps running if you close the page.
Try asking
“Is this phage temperate or virulent? Run BACPHLIP on the genome.”
Strengths and limits
Good at
- Available both as a standalone command-line application and as an importable Python library with modular functions.
- Native support for multi-record FASTA files to process multiple phage genomes in batch mode.
- Provides continuous probability values for both virulent and temperate predictions rather than simple binary flags.
Watch out for
- Requires complete phage genomes as input; incomplete or fragmented assemblies lack sufficient information and must not be used.
- Assumes all provided inputs are phage genomes, meaning non-phage DNA or bacterial chromosomes will yield misleading virulent or temperate classifications.
- Trained almost entirely on Caudovirales phages infecting Actinobacteria, Gammaproteobacteria, and Bacilli, requiring caution when applied outside these taxa.
Questions
Can I run BACPHLIP online without installing it?
Ask the research agent and it runs BACPHLIP as a job on a dedicated machine, then reads the results back to you. Nothing to install, and it keeps running if you close the page.
What licence is BACPHLIP under?
MIT. The terms are published at https://github.com/adamhockenberry/bacphlip.
Can BACPHLIP predict lifestyles from contigs or draft phage assemblies?
No. The absence of detected temperate domains is interpreted as evidence for a virulent lifestyle. If an assembly is partial or fragmented, critical lysogeny-associated domains may be missing from the sequence, causing false virulent classifications.
What happens if a non-phage sequence is provided as input?
BACPHLIP does not verify whether an input sequence is actually a bacteriophage. Random nucleotide sequences will typically be classified as virulent because they lack temperate domains, while whole bacterial chromosomes will likely be called temperate due to incidental domain matches.
What external tools must be installed before running BACPHLIP?
BACPHLIP requires the HMMER3 software suite (specifically the hmmsearch executable) to be accessible in the system path or supplied via a specific runtime flag.
What intermediate files are generated during a run?
The pipeline writes three intermediate files alongside the target FASTA: a six-frame translation file (.6frame), the raw HMMER output (.hmmsearch), and processed tabular domain hits (.hmmsearch.tsv).
How to cite it
Written from BACPHLIP's own README and project page. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.