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Phandango specifications

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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

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Maintainer


  • person_outline James Hadfield

Phandango citations

 (13)
library_books

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

2018
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 […]

library_books

Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species

2018
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 […]

library_books

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

2018
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 […]

library_books

Comparative Genomics of Bacteriophage of the Genus Seuratvirus

2017
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 autoani.pl with default settings (). all genome sequences were submitted to the ena under the project accession prjeb22133., the genomes of the 14 newly […]

library_books

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

2017
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 ). […]

library_books

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

2017
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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