Opening and saving sequences & alignments, Finding & obtaining sequences from remote databases, Using Non-UTOPIA or "legacy" CINEMA alignments
Alignment views, navigating an alignment, changing the level of detail, multiple views onto the same alignment, the consensus sequence, tool tips, the context menu
Inserting & removing gaps, sliding sequences, interacting with temporary groups of sequences, creating persistent sequence groups, the Sequence Group Manager, subdividing an alignment with breakpoints, changing the sequence order, removing sequences from an alignment, viewing different chains of PDB sequences
Defining a motif, editing a motif, re-validating a motif, using the Motif Manager, compiling a fingerprint of motifs, adding breakpoints to a motif, saving a motif as an image, printing a motif
The Annotations Manager, showing & hiding specific annotations, choosing different drawing styles for annotations, Changing the order of annotations, Resizing annotations
Access to remote bioinformatics services in CINEMA, Automatic alignment services, Sequence annotation services
Visualizing structure, highlighting regions in Ambrosia, showing annotations in Ambrosia
Basic searching, searching using regular expressions, fuzzy searching, search result-guided alignment
Printing an alignment, generating an image of an alignment, editing the colour scheme of an alignment