Hiding and Revealing Regions
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Use Window $\Rightarrow$ Close All in the desktop window menu to close all windows.
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Fetch the PFAM domain PF03460 alignment in PFAM (Seed) database by selecting File $\Rightarrow$ Fetch Sequences from desktop menu.
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Select a contiguous set of sequences by clicking and dragging on the sequence names in the sequence ID panel. With the sequence IDs selected, right-click the mouse to bring up the sequence ID context menu, and select Hide Sequences.
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Right-click on the blue triangle indicating hidden sequences, and select Reveal Sequences in the context menu. (If you have hidden all sequences then you will need to use the alignment window menu option View $\Rightarrow$ Show $\Rightarrow$ All Sequences.)
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Select a non-contiguous set of sequences using the [CTRL] ([CMD] on Mac) key and use the sequence ID context menu to hide them. Right-click on a blue triangle and select Reveal All in the context menu.
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With the [CTRL] ([CMD] on Mac) key pressed, click on several sequences’ IDs - both selected and unselected. Note how unselected IDs are added to the selection and previously selected IDs are individually deselected.
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In the alignment window menu, select View $\Rightarrow$ Show $\Rightarrow$ All Sequences to reveal the hidden sequences.
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Place cursor in alignment ruler above the sequences, repeat the above for columns to hide and reveal columns instead of sequences.
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With several columns selected, select View $\Rightarrow$ Hide $\Rightarrow$ All but selected region in the alignment menu.
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Reveal them using View $\Rightarrow$ Show $\Rightarrow$ All Columns. Use the [ESC] key to clear the selection.
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Select sequence representatives, select sequences by clicking and dragging on the sequence ID panel, hovering the mouse over the sequence ID to represent the rest by. Right click the mouse to open the context menu and selecting (Sequence ID name) $\Rightarrow$ Represent Group with (Sequence ID name). To reveal the sequences, right-click on the Sequence ID panel to open the context menu and select Reveal All. Use the [ESC] key to clear the selection.