Overview after aligning multiple genomes with Mauve

The Overview has different appearances, depending on the stage and workflow.

A Mauve genome alignment results in a set of locally colinear blocks (LCBs), each of which is a conserved region across multiple sequences. In MegAlign Pro, these may be referred to as “blocks” or “alignment blocks”. The Overview displays the part of a sequence in an alignment block as a “sequence block.” The sequence blocks in the same alignment block have the same color, and by default are shown connected by lines.

To orient the alignment around an active block, double-click on the sequence block. If necessary, individual sequences flip (i.e., are reverse complemented) to orient properly for the new alignment. Sequence rulers reorient along with the strands, and display the new coordinates. Gaps in the active block are shown by the presence of gray bars.

• Only one block is active at a time, and the current block for all the sequences blocks for are always shown in the forward orientation (i.e., on the top strand).

• Sequence blocks are usually displayed only if they include at least two sequences, though an exception is made when there is only one sequence in the project.

• Some sequences may not be included in the active block.

• In order to keep the current blocks in the same orientation, it may be necessary to reverse complement one or more entire genomes.

• The interior of the active block (only) displays a histogram of residue count, with gray areas representing gaps. These histograms reflect the proportion of non-gapped positions in a window corresponding to the number of positions spanned by a single pixel at a given zoom level.

• Blocks appearing out of order compared to other rows can signify an inversion. Blocks in reverse order compared to other rows can signify that the sequence is from the opposite strand compared to the other rows.

• If an alignment block is “hanging down” compared to other blocks in the same track, this signifies that the feature is encoded on the opposite strand. Having blocks represented on the lower strands are the result of rearrangements, such as inversions, and are not meant to imply that the alignment is double-stranded.

• The contents of the Distance and Tree views are specific to the active block only.

After aligning sequences end-to-end, vertical blue bars are used to show the beginnings and ends of the component sequences. These bars are displayed regardless of the type of alignment performed.