Alignment Window File Menu
- Add Sequences
Add sequences to the visible alignment from file, URL, or cut & paste
window
- 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.
- Save As
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.
- Export
Creates an alignment graphic with the current 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.
- 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.
Select the format of the text by selecting one of the following menu items.
- FASTA
- MSF
- CLUSTAL
- BLC
- PIR
- PFAM
- Print
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 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
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.