Alignment Window File Menu

• File
  
• 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.
  • HTML
    Create a web page from your alignment.
  • EPS
    Create an Encapsulated Postscript file from your alignment.
  • PNG
    Create a Portable Network Graphics file from your 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.
  
• 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.