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Phandango specifications


Unique identifier OMICS_14744
Name Phandango
Interface Web user interface
Restrictions to use None
Input data Phylogenetics trees, genome annotations, gubbins, brat nextgen, roary pan genome, scatterplots (manhattan plots)
Input format NEWICK, GFF3, TXT, CSV, PLINK
License MIT License
Computer skills Basic
Version 0.8.5
Stability Stable
Maintained Yes





  • person_outline James Hadfield

Phandango citations


Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica

PLoS Genet
PMCID: 5940178
PMID: 29738521
DOI: 10.1371/journal.pgen.1007333

[…] of the sequenced genomes leading to gene absence due to low coverage rather than true deletion or severe truncation. the relationship between invasiveness ranking and phylogeny were visualised using phandango []., we are grateful to sean eddy for useful discussions and providing fast, accurate and free software, and to simon harris for developing the pipeline used for mapping reads and calling […]


Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species

Nat Commun
PMCID: 5899146
PMID: 29654279
DOI: 10.1038/s41467-018-03949-8

[…] were then converted to fastq format, mapped to a draft assembly of an s. flexneri 2a major sublineage isolate, converted to a manhattan plot (again using seer inbuilt scripts) and visualised with phandango. this revealed a significant association of msma sublineage designation with pksr100 (fig. ). for comparison of the association of sequence elements detected for pksr100 and contiguous […]


The impact of serotype specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan genome

PLoS Pathog
PMCID: 5902063
PMID: 29617440
DOI: 10.1371/journal.ppat.1006966

[…] among scs using gubbins []. gubbins identifies snps introduced through recombination and allows censoring for downstream phylogenetic analysis. results of gubbins analyses were visualized using phandango []. for scs in which over 50% of the genome was censored due ancestral recombination events, we either sub-clustered scs clearly delineated monophyletic clades (e.g., sc19 […]


Comparative Genomics of Bacteriophage of the Genus Seuratvirus

Genome Biol Evol
PMCID: 5758909
PMID: 29272407
DOI: 10.1093/gbe/evx275

[…] fasttree v2.1.4 (). comparative genome analysis was carried out using roary, with “-i 50” (). a core-gene phylogeny was constructed using fasttree v2.1.4 (). core-gene data were visualized with phandango (). ani was calculated using with default settings (). all genome sequences were submitted to the ena under the project accession prjeb22133., the genomes of the 14 newly […]


Probing Genomic Aspects of the Multi Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors

Front Microbiol
PMCID: 5733095
PMID: 29312194
DOI: 10.3389/fmicb.2017.02485

[…] roary pangenome pipeline v3.6.1 to perform pangenomic analysis (page et al., ). roary was run with default parameters. a gene-absence-presence data matrix was subsequently derived and visualised in phandango genome visualizer (v0.87) (hadfield and harris, ). fripan was used to visualised mds clustering of isolates (supplementary figure ) and gene-presence-absence tree (supplementary figure ). […]


De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii

BMC Genomics
PMCID: 5644110
PMID: 29037147
DOI: 10.1186/s12864-017-4165-9

[…] when only a single methylase gene and a single motif were present or left unmatched. automatic pilus cluster search was performed using locp v. 1.0.0 []. the results were visualised with itol [], phandango 0.8.5 [], easyfig [] and pigeoncad []., all of the pcr reactions were performed with the phusion (thermofisher scientific) mastermix with 0.3% dmso and the primers prepared by oligomer oy […]

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