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Genome Comparator

Selecting 'All loci' will produce an artefactual analysis because this database contains different kinds of loci that are not equivalent (complete genes, MLST fragments, peptide variable regions, intergenic regions etc.). You are advised to select one of the recommended schemes.

Please select the required isolate ids and loci for comparison - use CTRL or SHIFT to make multiple selections in list boxes. In addition to selecting individual loci, you can choose to include all loci defined in schemes by selecting the appropriate scheme description. Alternatively, you can enter the accession number for an annotated reference genome and compare using the loci defined in that.

Isolates

User genomes

Optionally include data not in the
database.

Upload assembly FASTA file
(or zip file containing multiple
FASTA files - one per genome):

Loci

Include in identifiers

Recommended schemes

Select one or more schemes
below or use the full schemes list.

Schemes

All loci

Annotated reference genome Enter accession number:

or choose annotated genome:

or upload Genbank/EMBL/FASTA file:

Parameters / options

Min % identity:
Min % alignment:
BLASTN word size:
Rescan undesignated loci

Distance matrix calculation With incomplete loci:

Completely exclude from analysis
Treat as distinct allele
Ignore in pairwise comparison
Exclude pairwise missing loci
Exclude loci paralogous in all
Exclude pairwise paralogous loci

Alignments

Produce alignments
Include ref sequences in alignment
Align all loci (not only variable)
Create alignment stats
Aligner:

Core genome analysis

Core threshold (%):
Calculate mean distances

Filter by

Sequence method:
Project:
Experiment:

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