The tools located in the upper right of the Alignment view are used to accomplish the following tasks.

Task How to
To display the search tools To display the search tools in the upper left of the Alignment view, use the Find tool ( ).
To sort constituent sequences To sort read files (the files in the left margin of the view) according to the selected criteria, use the Sort reads tool ().

  • By Name – Sorts read files in alphanumeric order by name. This type of sorting is normally only used for Sanger reads, which are often user-named. This is a shortcut to the Sequence > Sort Reads > By Name command.

  • By Position – Sorts read files by their position along the consensus. This is a shortcut to the Sequence > Sort Reads > By Position command.

  • By Variant – Brings all the reads containing variant bases to the top of the alignment stack. This is a shortcut to the Sequence > Sort Reads > By Variant command. When you choose this option, SeqMan Ultra automatically loads and calculates the SNPs. Note that if you are working with a large .sqd project, this calculation can take a considerable amount of time.
To hide/show quality scores Use the Quality scores tool (). This tool only functions when a) trace data was used in the assembly.

  • Hide scores – Causes quality scores to be hidden from view.

  • Show scores – Causes quality scores to be displayed as a subscript next to the base. When bases with very high quality scores (>99% of the 95th percentile) are displayed, two asterisks (**) will be shown in place of the usual numerical subscripts. Example: G52 A84 G** C85.The quality score of a peak is calculated based on the shape and height of each peak and is adjusted relative to the maximum height of any peak in the entire sequence. Taller, sharper peaks receive the highest quality scores. The heights of any underlying peaks are subtracted from the highest peak’s score. Illumina data will typically have higher scores than Sanger data. For .fas files, SeqMan NGen automatically checks for .qual files with the same name in the same folder. If found, the quality values are displayed. Note that gaps are not assigned quality scores.

  • Show averaged scores – Displays quality scores averaged over a defined window. This mode is useful for examining trimming. Note that gaps are not assigned quality scores.
To adjust the zoom level Use the Compact text tool () to adjust the zoom level to maximize the number of bases while keeping the text legible. Use the Restore default zoom tool () to adjust the zoom level to the (wider) default setting, making the text more comfortable to read.
See how the sequence is anchored Prior to correcting an .sqd alignment with trace data (only), use the Anchor editing left (insert right) tool () to see how the sequence is anchored. If the left anchor is active, residues left of the insertion point are held in place. If you insert any characters, the downstream sequence slides to the right. If you delete any bases, the downstream sequence fills in the gap by sliding left. Use the Anchor editing right (insert left) tool () in a similar way.
Slide a Sanger sequence relative to other sequences Use the Allow sliding sequences tool (). When this tool is activated, the cursor is shaped like a banana. Use your mouse and the banana-shaped cursor to drag any sequence in the Alignment view to the left or right, as desired. When you are done, click the Banana tool again to return the cursor to its normal state. Note that this tool is only active when the alignment contains Sanger trace files.
To force SeqMan Ultra to call bases where ambiguity codes are currently displayed Use the Show/hide variant degeneracy tool (). To restore display of ambiguity codes, press the tool again.
Export data Use the Export data tool ( ). This tool acts as a shortcut to the File > Export Data > Consensus command and opens the same popup dialog. See Export data to a file for information on using the dialog.
Export image Use the Export image tool (). This tool acts as a shortcut to the File > Export Image > Alignment command. See Export an image of a view for more information.

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