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.
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.
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.
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.
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.
Sequence Bin Breakdown
Summary: Breakdown of sequence bin contig properties
The sequence bin breakdown plugin calculates statistics based on the number and length of contigs in the sequence bin as well as the number of loci tagged for each isolate record. Using this latter metric against a cgMLST scheme can be a good indicator of genome quality. Values for number of contigs, total sequence length, mean contig length and contig length distribution are charted.
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.
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).
Summary: Compare genomes at defined loci or against loci defined in a reference genome
Genome Comparator is used to compare whole genome data of isolates within the database using either the database defined loci or the coding sequences of an annotated genome as the comparator. Output is equivalent to a whole genome MLST profile, a distance matrix calculated based on allelic differences and a NeighborNet graph generated from this distance matrix. The analysis facilitates the determination of precisely which loci vary among isolates. Additionally, user-uploaded genomes that are not contained in the database can be analysed alongside genomes that are.
Summary: BLAST a query sequence against selected isolate data
The BLAST plugin enables you to BLAST a sequence against any of the genomes in the database, displaying a table of matches which can be downloaded in Excel format. In addition, the matched sequence regions are made available for download in FASTA format, either with or without surrounding flanking sequence.
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.
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.