Main window (back to Contents)

  1. Overview - A miniature view of the entire phylogenetic tree and SNP heatmap, with the currently zoomed sections of each highlighted in blue.

  2. Annotations - If a GenBank file was provided, its annotations will appear here. When zoomed out, they are condensed into a density plot. Hover over genes to show more information, and click on them to zoom. This view also shows LCB boundaries (gray lines; faded out if crowded), and reference contig boundaries (red lines).

  3. Ruler - Reference-based (ungapped) positions for the current view. Click to re-center; click and drag to zoom in on a region.

  4. SNP totals / reference - When zoomed out, shows SNP density, summed by alignment column and scaled by its own maximum within the current zoom. When zoomed in, shows the reference sequence.

  5. Phylogenetic tree - Use the scroll wheel or click to zoom in on particular clades. To zoom out, use the scroll wheel or click wherever the cursor is an up-arrow (outside zoomable clades). Click on a leaf to enlarge the surrounding leaves, and click again to shrink. Right-click to:

  6. SNP heatmap - Shows SNP density across each genome, scaled by the maximum density at the current zoom. Zoom in with the scroll wheel to see more detail or alignments. Click a track to enlarge the surrounding tracks, and click again to shrink. Right-click to set a track as the variant reference.

  7. Selected genome - If genomes are too condensed to see, they can be clicked on (either in the phylogenetic tree or the SNP heatmap) to expand them and their neighbors. Click the selected genome again to unselect.

  8. Genome name - The name of the genome currently under the cursor.

  9. Branch length - The phylogenetic branch length of the leaf or other node currently under the cursor.

  10. Bootstrap - The bootstrap value of the phylogenetic node currently under the cursor.

  11. Track count - The number of genomes in the alignment or leaves in the tree.

  12. Core percentage - Shows the percentage of the reference that is covered by core alignments, colored by expected ranges. At or above 50% is good (green); at or above 30% is marnigal (yellow); below 30% (red) should be scrutinized.

  13. Reference position - The (ungapped) reference position currently under the cursor. This position will not change in insertions relative to the reference genome (see "Insertion offset").

  14. Insertion offset - If the cursor is over an insertion relative to the reference, the current position within it, starting from 1 at the first inserted position.

  15. Heatmap legend - The color gamut of the SNP heatmap, with increasing SNP density from left to right. The rightmost color represents densities beyond the current maximum, which can be seen in the heatmap when adjusting filters in the Variant window. When zoomed to alignments, the legend will show nucleotide color codes, with reference nucleotides on the left and variants (matching the current filter settings) to the right.

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