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Phamerator specifications


Unique identifier OMICS_22327
Name Phamerator
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Database management system MySQL
Computer skills Medium
pyro, clustalw, python-biopython, mysql-server, python-mysqldb, python-pygoocanvas, curl
Maintained No


No version available


This tool is not maintained anymore.

Publication for Phamerator

Phamerator citations


Genome Sequences of Ilzat and Eleri, Two Phages Isolated Using Microbacterium foliorum NRRL B 24224

Genome Announc
PMCID: 5897797
PMID: 29650566
DOI: 10.1128/genomeA.00144-18

[…] that of the isolation host (68.7%; GenBank accession no. JYIU00000000).The genomes were annotated using DNA Master (, Glimmer (), GeneMark (), BLASTP (), HHpred (), and Phamerator (). A total of 62 and 63 protein-coding genes were identified in Ilzat and Eleri, respectively. The two phages share similar genome architectures and synteny, with DNA packaging, virion str […]


Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages

BMC Microbiol
PMCID: 5831693
PMID: 29490612
DOI: 10.1186/s12866-018-1159-y
call_split See protocol

[…] were analyzed and annotated using the genome editor DNAMaster ( GenBank accession numbers are listed in Table . Genome comparisons were performed and represented using Phamerator and the database ‘Actinobacteriophage_685’ []. […]


Genomic Sequence of Mycobacteriophage OKCentral2016

Genome Announc
PMCID: 5824014
PMID: 29472341
DOI: 10.1128/genomeA.01208-17

[…] n-coding regions of the genome were detected using Glimmer () and GeneMark (). Starterator ( was used to evaluate gene start codons. Gene function was determined using Phamerator () and BLASTn/BLASTp on ARAGORN () and tRNAscan-SE () were used to analyze tRNA sequences within the genome. OKCentral2016 was shown to possess 84 protein-coding genes and 1 t […]


Complete Genome Sequence of Cluster J Mycobacteriophage Superphikiman

Genome Announc
PMCID: 5794948
PMID: 29437101
DOI: 10.1128/genomeA.01538-17

[…] efense systems. Other cluster J bacteriophages such as Courthouse have short reverse genes in this position; however, the number of genes present and the nucleotide sequences vary across this region ( The immunity repressor in Superphikiman (gp191) is identical to the immunity repressor genes found in the cluster A1 bacteriophages Dynamix (gp75) (GenBank accession number AMD43071) […]


Genome Sequence of a Newly Isolated F2 Subcluster Mycobacteriophage from the Black Belt Geological Region of Western Alabama

Genome Announc
PMCID: 5786693
PMID: 29371367
DOI: 10.1128/genomeA.01555-17

[…] the F2 subcluster is 56,236 bp, and the average gene number is 111. Demsculpinboyz and other F2 phages show high nucleotide similarity and share a conserved region in the first third of the genome. A Phamerator map of Che9d and Demsculpinboyz shows a decrease in nucleotide similarity at 30,000 bp ().Within the F2 subcluster, the Lysin A gene (Demsculpinboyz gp35) is represented by three variations […]


The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile

Front Microbiol
PMCID: 5786514
PMID: 29403466
DOI: 10.3389/fmicb.2018.00026

[…] confirmed this finding, as only a low fraction of the genes was conserved in the phiCD5763-like phages (15%, 55/364), the phiCD2955-like phages (20%, 66/338), or all 10 big phage genomes (3%, 15/538).Phamerator defined 328 phams from the 10 big phage genome assemblies (Supplementary Material ). Sixty-six of these phams were omnipresent among phiCD5763-like and phiCD2955-like phage genomes (20%), b […]


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Phamerator institution(s)
Department of Biology, James Madison University, Harrisonburg, VA, USA; Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
Phamerator funding source(s)
Supported in part by a grant to the University of Pittsburgh by the Howard Hughes Medical Institute (HHMI) under HHMI’s Professors program; and by grants from NIH (GM51975), (GM093901) and (AI082527).

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