Analysis plugins

Categories - Jump to: Breakdown | Analysis | Third party


Breakdown plugins - Jump to: Field Breakdown | Two Field Breakdown | Unique Combinations | Polymorphisms | Publication Breakdown

Field Breakdown

Summary: Breakdown of query results by field

The field breakdown plugin displays the frequency of each value for fields, alleles and schemes. Output is in the form of dynamic charts, maps, and tables. Data can be exported as an Excel file, SVG image, or FASTA file.


Launch 'Field Breakdown'

Two Field Breakdown

Summary: Breakdown of one field against another

The two field breakdown plugin generates a table breaking down the frequencies of one field against another. This is analagous to a spreadsheet pivot table. Any primary metadata field, locus, or scheme field can be used and the output can be exported as an Excel spreadsheet.


Launch 'Two Field Breakdown'

Unique Combinations

Summary: Determine frequencies of unique field combinations

The Unique Combinations plugin calculates the frequencies of unique file combinations within an isolate dataset. Primary metadata fields, allele designations and scheme fields can be combined. Results are returned in an Excel spreadsheet.


Launch 'Unique Combinations'


Summary: Tool for analysing polymorphic sites for particular locus in an isolate dataset

This plugin generates a schematic of the selected locus showing all the polymorphic sites present in the selected dataset. These are also shown in a tabular form with precise frequencies for each nucleotide at every position.


Launch 'Polymorphisms'

Publication Breakdown

Summary: Breakdown of query results by publication

This plugin shows all publications linked to isolates in a query dataset or within the whole database. The results can be filtered by author or year. The output includes full citation details and a link to display all isolates linked to any listed publication.


Launch 'Publication Breakdown'


Analysis plugins - Jump to: BURST | Codon Usage | Gene Presence


Summary: Perform BURST cluster analysis on query results query results

BURST is an algorithm used to group MLST-type data based on a count of the number of profiles that match each other at specified numbers of loci. The analysis is available for both sequence definition database and isolate database schemes that have primary key fields set. Analysis is limited to 1000 or fewer records.


Launch 'BURST'

Codon Usage

Summary: Determine codon usage for specified loci for an isolate database query

The codon usage plugin calculates the absolute and relative synonymous codon usage by isolate and by locus for any dataset or the whole database. Specific loci or the loci that are members of a particular scheme can be chosen for analysis.


Launch 'Codon Usage'

Gene Presence

Summary: Analyse presence/absence of loci for dataset generated from query results

The Gene Presence analysis tool will determine whether loci are present or absent, incomplete, have alleles designated, or sequence regions tagged for selected isolates and loci. If a genome is present and a locus designation not set in the database, then the presence and completion status are determined by scanning the genomes. The results can be displayed as interactive pivot tables or a heatmap. The analysis is limited to 500,000 data points (locus x isolates).


Launch 'Gene Presence'

Third party

Third party plugins - Jump to: GrapeTree | iTOL | ReporTree


Summary: Visualization of genomic relationships

GrapeTree is a tool for generating and visualising minimum spanning trees (Zhou at al. 2018 Genome Res 28:1395-1404). It has been developed to handle large datasets (in the region of 1000s of genomes) and works with 1000s of loci as used in cgMLST. It uses an improved minimum spanning algorithm that is better able to handle missing data than alternative algorithms and is able to produce publication quality outputs. Datasets can include metadata which allows nodes in the resultant tree to be coloured interactively.


Launch 'GrapeTree'


Summary: Phylogenetic trees with data overlays

The ITOL plugin allows you to generate and visualise phylogenetic trees calculated from concatenated sequence alignments of selected loci (or the loci belonging to a particular scheme). Currently, only Neighbour-joining trees are supported. Datasets can include metadata which allows nodes in the resultant tree to be coloured. Datasets are uploaded to the Interactive Tree of Life website (Letunic & Bork 2016 Nucleic Acids Res 44(W1):W242-5) for visualisation.


Launch 'iTOL'


Summary: Surveillance-oriented tool to strengthen the linkage between pathogen genetic clusers and epidemiological data

A pivotal outcome of genomics surveillance is the identification of pathogen genetic clusters/lineages and their characterization in terms of geotemporal spread or linkage to clinical and demographic data. This task usually relies on the visual exploration of (large) phylogenetic trees (e.g. Minimum Spanning Trees (MST) for bacteria or rooted SNP-based trees for viruses). As this may be a non-trivial, non-reproducible and time consuming task, we developed ReporTree, a flexible pipeline that facilitates the detection of genetic clusters and their linkage to epidemiological data. It is described in Mixão et al. 2023 Genome Med 15:43.


Launch 'ReporTree'