View alignments

Since an alignment is a display of several sequences arranged in rows, the basic options for viewing alignments are the same as for viewing sequences. Therefore we refer to View sequences for an explanation of these basic options.

However, there are a number of alignment-specific view options in the Alignment info and the Nucleotide info

in the Side Panel to the right of the view. Below is more information on these view options.

Under Translation in the Nucleotide info, there is an extra checkbox: Relative to top sequence. Checking this box will make the reading frames for the translation align with the top sequence so that you can compare the effect of nucleotide differences on the protein level.

The options in the Alignment info relate to each column in the alignment.


Shows a consensus sequence at the bottom of the alignment. The consensus sequence is based on every single position in the alignment and reflects an artificial sequence which resembles the sequence information of the alignment, but only as one single sequence. If all sequences of the alignment is 100% identical the consensus sequence will be identical to all sequences found in the alignment. If the sequences of the alignment differ the consensus sequence will reflect the most common sequences in the alignment. Parameters for adjusting the consensus sequences are described below.

The Consensus Sequence can be opened in a new view, simply by right-clicking the Consensus Sequence and click Open Consensus in New View.


Displays the level of conservation at each position in the alignment. The conservation shows the conservation of all sequence positions. The height of the bar, or the gradient of the color reflect how conserved that particular position is in the alignment. If one position is 100% conserved the bar will be shown in full height, and it is colored in the color specified at the right side of the gradient slider.

Gap fraction

Which fraction of the sequences in the alignment that have gaps. The gap fraction is only relevant if there are gaps in the alignment.

Color different residues

Indicates differences in aligned residues.

Sequence logo

A sequence logo displays the frequencies of residues at each position in an alignment. This is presented as the relative heights of letters, along with the degree of sequence conservation as the total height of a stack of letters, measured in bits of information. The vertical scale is in bits, with a maximum of 2 bits for nucleotides and approximately 4.32 bits for amino acid residues. See Bioinformatics explained: Sequence logo for more details.