Alignment Window File Menu
- Fetch Sequence
Shows a dialog window in which you can select known ids from
Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by
the European Bioinformatics Institute. See Sequence Fetcher.
- Add Sequences
Add sequences to the visible alignment from file, URL, or cut &
paste window
- Reload
Reloads the alignment from the original file, if available.
Warning: This will delete any edits, analyses and
colourings applied since the alignment was last saved, and cannot be
undone.
- Save (Control S)
Saves the alignment to the file it was loaded from (if available), in
the same format, updating the original in place.
- Save As (Control Shift S)
Save the alignment to local file. A file selection window will
open, use the "Files of type:" selection box to determine
which alignment format to save as.
- Output to Textbox
The alignment will be displayed in plain text in a new window,
which you can "Copy and Paste" using the pull down menu, or
your standard operating system copy and paste keys. The output window
also has a "New Window" button to import the
(possibly edited) text as a new alignment.
Select the format of the text by selecting one of the following menu
items.
- FASTA
- MSF
- CLUSTAL
- BLC
- PIR
- PFAM
- Print (Control P)
Jalview will print the alignment using the current fonts and
colours of your alignment. If the alignment has annotations visible,
these will be printed below the alignment. If the alignment is wrapped
the number of residues per line of your alignment will depend on the
paper width or your alignment window width, whichever is the smaller.
- Export Image
Creates an alignment graphic with the current view's annotation,
alignment background colours and group colours. If the alignment is wrapped, the output will also be
wrapped and will have the same visible residue width as the open
alignment.
- Export Features
All features visible on the alignment can be saved to file or displayed
in a textbox in either Jalview or GFF format
- Export Annotations
All annotations visible on the alignment can be saved to file or
displayed in a textbox in Jalview annotations format.
- Load Associated Tree
Jalview can view
trees stored in the Newick file format, and associate them with the
alignment. Note: the ids of the tree file and your alignment MUST be
the same.
- Load Features / Annotations
Load files describing precalculated sequence features or alignment annotations.
- Close (Control W)
Close the alignment window. Make sure you have saved your
alignment before you close - either as a Jalview project or by using
the Save As menu.