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CHAPTER 14. SEQUENCE ALIGNMENT
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Background color. Sets a background color of the residues using a gradient in the
same way as described above.
Graph. Displays the gap fraction as a graph at the bottom of the alignment (Learn how
to export the data behind the graph in section 6.4).
∗ Height. Specifies the height of the graph.
∗ Type. The type of the graph.
· Line plot. Displays the graph as a line plot.
· Bar plot. Displays the graph as a line plot.
· Colors. Displays the graph as a color bar using a gradient like the foreground
and background colors.
∗ Color box. Specifies the color of the graph for line and bar plots, and specifies a
gradient for colors.
• Color different residues. Indicates differences in aligned residues.
Foreground color. Colors the letter.
Background color. Sets a background color of the residues.
14.3
Edit alignments
14.3.1
Move residues and gaps
The placement of gaps in the alignment can be changed by modifying the parameters when
creating the alignment (see section 14.1). However, gaps and residues can also be moved after
the alignment is created:
select one or more gaps or residues in the alignment | drag the selection to move
This can be done both for single sequences, but also for multiple sequences by making a
selection covering more than one sequence. When you have made the selection, the mouse
pointer turns into a horizontal arrow indicating that the selection can be moved (see figure 14.5).
Note! Residues can only be moved when they are next to a gap.
Figure 14.5: Moving a part of an alignment. Notice the change of mouse pointer to a horizontal
arrow.
14.3.2
Insert gaps
The placement of gaps in the alignment can be changed by modifying the parameters when
creating the alignment. However, gaps can also be added manually after the alignment is