Multiple sequence alignments can be constructed in the following ways.
Align the sequences of a set of orthologs by visiting the gene page for one of the genes,
clicking the right-sidebar menu item Align Gene Nucleotide Sequence with Orthologs (or
Align Gene Product Amino Acid Sequence with Orthologs), and selecting
the organisms from which orthologs should be obtained. The alignment will be
computed by Clustal Omega.
Construct a SmartTable containing the genes or proteins you wish to align, then run one
of the following commands from the right-sidebar menu for that SmartTable:
Column → View Alignment of Gene Nucleotide Sequences or Column → View Alignment of Gene Product Peptide Sequences.
The alignment will be computed by Clustal Omega.
Align a set of arbitrary nucleotide sequence regions and
optional other nucleotide sequences by
entering the organism and start/end coordinates for each sequence
region into the form created by clicking this button. To add
the coordinates for a particular gene, search for the gene and
then click the plus icon to insert the gene start and/or end
coordinates with optional upstream or downstream offsets.