Deselect menu – Every time you use a right-click ‘Select’ option on a nucleotide in the multiple alignment (and also when you use the ‘Assemble consistent reads’ function, below), your selections are added to a list. Clicking this button opens the “Remove Selections” window showing the list of selections, sorted by reference position, and allows you to remove any or all of the selections (Figure 1‑61). As the selections are removed, the sequences hidden by those selections will be added back to the multiple alignment.

Declare project variant – Clicking this button takes the current set of ‘Select’ choices you made on the multi-alignment, and converts it into a new Variant on the Variants sub-tab of the Project Tab; this Variant will then be searched for during the next computation, with reporting of the search results in the Variants Tab. An “Approve new variant” window (Figure 1-62) will first open and show how your ‘Select’ choices have been converted into a valid ‘Pattern’ compatible with the Variant scanning function; the ‘Reference’ Sequence will have been determined based on the alignment you were viewing. The window also has fields in which you can select a Status for the Variant from a drop down (defaults to Accepted) and in which you can enter a Name and an Annotation for the new Variant, before accepting it. If the Pattern is equivalent to that of a Variant already defined in the Project, the window will display a warning of this fact to help prevent the incorporation of a redundant Variant.

Keep in mind that during Variant scanning, a read must overlap all the positions involved in the Variant to qualify as containing the Variant, so the ‘Select’ choices should be as compact and succinct as possible before declaring a Variant. Note also that there must be at least one ‘Select’ choice made prior to clicking the ‘Declare project variant’ button or the ‘Approve new variant’ window will not open. In some cases, the current selections may be close to, but not exactly, the Variant Pattern you want to use to define the new Variant. The “Approve new variant” window does not, however, let you edit the synthesized Variant Pattern. In this case, you should approve the addition of the Variant to the Project and subsequently edit it in the Variants sub-tab of the Project Tab (section 1.3.2.5).

Since possible Variants are automatically proposed by the AVA software, potentially in quite large numbers, the software attempts to provide meaningful but unique default names (see section 4.2). This also applies to Variants declared manually, via the Approve New Variant window.

Assemble consistent reads – This button provides a means of mining for consistent patterns out of the sequences in the multiple alignment. “Consistent reads” means reads that are identical in the portion over which they overlap (i.e. overhanging nucleotides due to reads of different lengths do not penalize the “consistency”). This is more useful when the ‘Read Type’ is set to ‘Individual’ as opposed to ‘Consensus’ (in which case the consensus process has already gathered up similar reads). Using the reads on display in the multiple alignment as input (but not those already hidden away by ‘Select’ choices), the assembly process makes a set of automated ‘Select’ choices to identify sets of consistent reads for display.

Remove reads, reset selections – Clicking this button takes all the displayed sequences in the multiple alignment to the right and discards them from memory. The full set of alignment position filters is cleared, and any remaining sequences that were hidden by prior selections are revealed in the alignment. This button is typically used in conjunction with the ‘Assemble consistent reads’ button described above, as a means to recursively mine for patterns in the alignment. Once you click this button you cannot undo the sequence discard, but the sequences are only discarded from memory and not from the underlying multiple alignment. Reopening the global alignment via the Project Trees or the Variants Tab, or using the “Alignment data” display control tools (section 1.6.4.1), will reload the original alignment and restore the full complement of reads or consensi. (Similarly, if you are in the Consensus Align tab, you can restore the full complement of reads by returning to the Global Align tab and re-loading the same consensus; see section 1.7.)

Save table snapshot to image file – This button saves the visible portion of the multiple sequence alignment at the right as a PNG image file. A file browser window will open, allowing you to assign a name and a destination for the file.

Save the alignment as ... – This button takes the multiple sequence alignment at the right and writes it out as a FASTA, Clustal, Ace, SAM, BAM*, or Table (csv or tsv) formatted file, so you can import it into a suitable third-party application. A file browser window will open, allowing you to choose the file type. A filename with the appropriate extension is automatically generated, but you are free to rename it. You should maintain the standard file suffixes since some applications will expect them when importing the file.