Hidden Regions
Use the keyboard key "H" to hide / reveal selected columns and sequences. To hide / reveal only selected sequences, use "Shift H", to hide / reveal only selected columns, use "Control H".
Hiding Sequences
To hide selected sequences in an alignment, use the "View
-> Hide -> Selected Sequences" menu item or simply select "Hide
Sequences" from the Popup menu after a right click on the sequence Ids.
Hidden sequences will not be used in any calculations, editing or web service alignments performed on visible sequences.
Hidden Sequences Representatives
A more advanced hide involves a right-mouse click on a sequence, then selecting
"SequenceID -> Represent Group with SequenceId". Using this method
of hiding sequences, any edits performed on the visible group representative
will be propogated to all the sequences in that group.
The hidden representative sequences will not be used in any
calculations or web service alignments (nb. this may change in
the future)
Hiding Columns
To hide selected columns in an alignment, use the "View
-> Hide -> Selected Columns" menu item, or right click within a region
of selected columns in the scale above the alignment (only available in non
wrapped mode) and select "Hide Columns".
When an alignment view contains hidden columns, certain constraints apply:
Column Separability
Calculations where hidden columns are
excluded, and a single analysis performed on the result, are termed column-separable.
The simple Tree and PCA calculations are column separable because essentially the same results
would be obtained if the excluded hidden columns were replaced by gaps as the input to the calculation.
Multiple Sequence alignment and secondary structure prediction are both non-column-separable, and so the exclusion of hidden regions leads to only 'locally optimal' results - sometimes different to that obtained when using the full alignment.