MLST Scheme Visualization and Management

A MLST Scheme contains information about:

The MLST Scheme has several views. Switching between the views of the scheme is done by clicking the buttons at the lower-left corner of the view.

Image lmlst_heatmap
Figure 12.1: The MLST Scheme Heat Map view.

The heat map view shows an overview of the scheme (figure 12.1), with the sequence types on the vertical axis, and the loci on the horizontal axis. Each cell in the heat map is colored according to the frequency of the allele in the given locus, that is, a value of 0.9 means 90% of the sequence types have this particular allele. Missing alleles will have a value of zero, alleles not present in any sequence type are not represented by the heat map view. The heat map can optionally be clustered based on the allele frequency. The clustering settings can be specified at scheme creation time, but it is also possible to use the Recluster MLST scheme button to update the clustering.

By right-clicking on the heat map, it is possible to either select sequence types or loci in other views or copy sequence or loci names to the clipboard.

Image mlst_allele_table
Figure 12.2: The Allele table view.

The allele table view (figure 12.2) has an upper table that lists the loci in the scheme. The table contains the following columns:

The lower table lists the alleles for the selected loci. It has the following columns:

It is possible to Align Selected Alleles, which creates a new multiple sequence alignment view or to Extract Selected Alleles, which creates a sequence list with the alleles.

Image mlst_sequence_type_table
Figure 12.3: The Sequence Type table.

The Sequence Type table view (figure 12.3) shows the sequence types in the scheme. It always contains the following columns:

Several other columns with arbitrary metadata information may be present as well.

At the bottom of the view, two buttons make it possible to Select Sequence Types in Other Views and to Create Large Sub Scheme.

Image mlst_subscheme
Figure 12.4: The Create MLST Subscheme options.

The Create Large Sub Scheme has the same options (figure 12.4) as the other scheme creation tools, except for some additional options for pruning the scheme:

Finally, the MLST Scheme also has a Minimum Spanning Tree view, which is the topic of the next section.