FriPan statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Genome viewers chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

Protocols

To access compelling stats and trends, optimize your time and resources and pinpoint new correlations, you will need to subscribe to our premium service.

Subscribe

FriPan specifications

Information


Unique identifier OMICS_03550
Name FriPan
Interface Web user interface
Restrictions to use None
License GNU General Public License version 3.0
Computer skills Basic
Stability Stable
Requirements
CoffeeScript
Maintained Yes

Download


Additional information


http://drpowell.github.io/FriPan/example/

FriPan in pipeline

2015
PMCID: 4592193
PMID: 26431321
DOI: 10.1371/journal.pone.0138527

[…] reciprocal similarity searches of all predicted and expressed proteins were performed using blast algorithm [], as well as proteinortho5 tool [] followed by the visualization of results using fripan (http://www.vicbioinformatics.com/software.fripan.shtml)., carbon source utilization was assessed by growing bacteria in m9 minimal medium (sigma) with the addition of the substrate […]


To access a full list of citations, you will need to upgrade to our premium service.

FriPan in publications

 (7)
PMCID: 5733095
PMID: 29312194
DOI: 10.3389/fmicb.2017.02485

[…] (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 ). recommended r scripts from roary package were used to generate […]

PMCID: 5447721
PMID: 28611758
DOI: 10.3389/fmicb.2017.00961

[…] the best blast alignments. the clusters of orthologous genes (ogs) present in all strains were determined as the core genes of p. multocida. distribution of ogs among strains was visualized by using fripan (https://github.com/drpowell/fripan). using blastp functional annotation and classification of ogs were performed based on the uniref50 database (suzek et al., ), the cluster of orthologous […]

PMCID: 5267571
PMID: 28149688
DOI: 10.7717/peerj.2916

[…] reciprocal blast using proteinortho5 v5.11 (). a blast cutoff of 95% identity and alignment coverage of 30% were used. the resulting matrix of ortholog presence and absence was visualized using fripan (https://github.com/drpowell/fripan) (downloaded on the 28th of april 2016). the general feature format files have been deposited in figshare […]

PMCID: 5333547
PMID: 28265515
DOI: 10.7717/peerj.3047

[…] reads with accession numbers ers1354589-600 have been deposited in the european nucleotide archive (ena), project prjeb15428. ortholog clustering was performed using roary () and was visualized with fripan (http://drpowell.github.io/fripan/). recombination within the core genome was inferred using clonalframeml v1.7 () with the whole genome alignment generated by nullarbor. using fasttree v2.1.8 […]

PMCID: 5537629
PMID: 28785416
DOI: 10.1099/mgen.0.000077

[…] pangenome analysis, protein ortholog clustering was performed using proteinortho v5.11(), alignment of the resultant cds orthologs to bph0662 and visualisation of the pangenome was performed using fripan ()., e. coli mutants expressing the bph0662 type i rm systems in a dc10b background were created using the method previously described by . e. coli dc10b-ms1, which expressed sepibph0662i […]


To access a full list of publications, you will need to upgrade to our premium service.

FriPan review

star_border star_border star_border star_border star_border
star star star star star

Korin Albert

star_border star_border star_border star_border star_border
star star star star star
Web
I use FriPan to visualize the pangenome output from Roary. It's easy once you adjust your Roary data using roary2fripan (https://github.com/kwongj/roary2fripan). This is web-based in the sense that you view it in a web browser, but it requires more knowledge to set up than a website like RAST. But once you set it up, you can view a heatmap-like figure of the genomes in your pangenome and then zoom in on specific loci with strain differences.