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.

Task How to…
Specify which statistical values appear in the upper-right of the table Use the Upper right drop-down menu 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).

  • %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.

  • 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.

Notes:

  • Similarity metrics always use BLOSUM62 for protein alignments. 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.
Specify which statistical values appear in the bottom-left of the table Use the Lower left drop-down menu to choose from the same options listed just above.
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.
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.

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