The Distance section affects the appearance of the Distance view. To access this section, click on the Style panel expand bar entitled Distance, or choose View > Style > Distance.
|Specify which statistical values appear in the table
|| Use the Values drop-down menu in the Upper right and Lower left sections to choose from:
- Distance – A number between 0 and 1, with 0 being an exact match and 1 indicating no matching bases at all.
- %Identity – 100% * (Number of identical bases, excluding ambiguous bases) / (The number of aligned pairs of bases considered during computation of distance).
- %Similar – 100% * (Number of matching bases, including ambiguous bases that may be a possible match) / (The number of aligned pairs of bases considered during computation of distance).
- %Dissimilar – 100% – %Similar (see above).
- %Gaps – 100% * (Gap count / (Gaps + Length)).
- Identical – Number of identical bases, excluding ambiguous bases.
- Similar – Number of matching bases, including ambiguous bases that may be a possible match.
- Dissimilar – Total number of bases – Similar (see above).
- Gap count – Number of aligned positions in the two sequences in which at least one is a gap.
- Gap length – Length of regions in which at least one of the two sequences has a gap.
- Length – The number of aligned pairs of bases considered during computation of distance.
- You can alternatively choose the distance metrics to display using the drop-down menus in the upper left of the Distance view.
- Similarity is measured on aligned pairs of amino acids, with the help of the BLOSUM62 substitution matrix. A pair is similar if the substitution matrix has a positive value for the pair. A positive value in BLOSUM62 indicates a more likely substitution. The substitution matrix chosen for the alignment method, if any, does not affect the similarity measure in the distance table.
- Statistics are calculated across the entire alignment, regardless of where the sequences overlap.
- With global gap removal, positions ignored because they’re global gaps are not considered in the statistics. All and only pairwise gaps are reflected.
|Add heat map coloration to the table
|| Check the Heat map boxes corresponding to the Upper right and/or Lower left sections of the table.
- To select a color for either end, click on the end of the colored bar corresponding to a section and make a selection from the color picker.
- To flip the direction of the gradient, click on the left of the two corresponding Flip gradient tools (). If the gradient went from white to dark blue, for example, it will now go from dark blue to white. By default, the gradient progresses linearly from 0-100%.
- To better see lower or higher values, click on the right of the two corresponding Flip gradient tools ( ) and select Distinguish lower values better or Distinguish higher values better. To return to a linear progression, choose Normal.
|Specify the Distance view font style
|| Use the Font menu to choose between seven available fonts. Recently selected fonts (if any) appear at the top of the menu, and other available fonts appear below the row of dashes.
|Specify the Distance view font size
|| Type a number to the right of Font or use the corresponding up and down arrows ( ) to select a font size. Allowed values = 4 to 72. To make the font Bold and/or Italic, press the B and/or I buttons, respectively.
|Specify the number of decimal places displayed in the Distance view
|| Type a number to the right of Decimal places, or use the corresponding up and down arrows ( ) to specify the number of decimal places. Allowed values = 1 to 7.