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: