ArticleG3 (Bethesda, Md.)2022
PhaMMseqs: a new pipeline for constructing phage gene phamilies using MMseqs2.
Article in G3 (Bethesda, Md.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Mycobacteriophage Adephagia gp48 inhibits essential host cell wall biosynthesis enzyme mannose-1-phosphate guanylyltransferase.bioRxiv : the preprint server for biology · 2026Article
- Human Gut Phageome Analysis Uncovers Thousands of Highly Modular Endolysins.MicrobiologyOpen · 2026Article
- Genomic landscape of completeFrontiers in microbiology · 2026Article
- Complete Genome Sequences of Eleven Cluster DJmicroPublication biology · 2026Article
- Characterization and Therapeutic Potential of a Novel Bacteriophage Targeting Methicillin-ResistantInternational journal of microbiology · 2026Article
- Article
- Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes.Nature microbiology · 2026Article
- Article
- Bacteriophage resistance evolution in a honey bee pathogen.Microbiology (Reading, England) · 2025Article
- Diversity and Role of Prophages inGenes · 2025Article
- Genome-wide screen overexpressing mycobacteriophage Amelie genes identifies multiple inhibitors of mycobacterial growth.G3 (Bethesda, Md.) · 2025Article
- Complete Genome Sequence of the Cluster DJ Actinobacteriophage, Petito, isolated on the hostmicroPublication biology · 2025Article
- How to introduce a new bacteriophage on the block: a short guide to phage classification.Journal of virology · 2024Review
- Complete genomes of two cluster AKMicrobiology resource announcements · 2024Article
- Genome sequence of Xenia2 a DV cluster phage that infectsMicrobiology resource announcements · 2024Article
- Characterization of mycobacteriophage Adephagia cytotoxic proteins.G3 (Bethesda, Md.) · 2024Article
- A Bioinformatic Ecosystem for Bacteriophage Genomics: PhaMMSeqs, Phamerator, pdm_utils, PhagesDB, DEPhT, and PhamClust.Viruses · 2024Review
- Introducing Casbah, Kronus, and MmasiCarm, Members of the Mycobacteriophage Subcluster B3.PHAGE (New Rochelle, N.Y.) · 2024Article
- A genome-wide cytotoxicity screen of cluster F1 mycobacteriophage Girr reveals novel inhibitors of Mycobacterium smegmatis growth.G3 (Bethesda, Md.) · 2024Article
- A genome-wide overexpression screen reveals Mycobacterium smegmatis growth inhibitors encoded by mycobacteriophage Hammy.G3 (Bethesda, Md.) · 2023Article
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Authors and funding
3 authors.
Funding
Abstract
The diversity and mosaic architecture of phage genomes present challenges for whole-genome phylogenies and comparative genomics. There are no universally conserved core genes, ∼70% of phage genes are of unknown function, and phage genomes are replete with small (<500 bp) open reading frames. Assembling sequence-related genes into "phamilies" ("phams") based on amino acid sequence similarity simplifies comparative phage genomics and facilitates representations of phage genome mosaicism. With the rapid and substantial increase in the numbers of sequenced phage genomes, computationally efficient pham assembly is needed, together with strategies for including newly sequenced phage genomes. Here, we describe the Python package PhaMMseqs, which uses MMseqs2 for pham assembly, and we evaluate the key parameters for optimal pham assembly of sequence- and functionally related proteins. PhaMMseqs runs efficiently with only modest hardware requirements and integrates with the pdm_utils package for simple genome entry and export of datasets for evolutionary analyses and phage genome map construction.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.