Alignment Window File Menu

- Fetch Sequence
  Shows a dialog window in which you can select known ids from UniProt, EMBL, EMBLCDS, PDB, PFAM, or RFAM databases 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
  - PileUp
  - AMSA
  - STH
  - PHYLIP
  - JSON
- Page Setup ...
  Open the printing system's Page Setup dialog box, to control page size, layout and orientation.
- 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.
  - 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.
  - SVG
    Create a Scalable Vector Graphics file from your alignment for embedding in web pages.
  - BioJS
    Create a BioJS MSA Viewer HTML file from your 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.
- Load VCF File
  Load VCF annotations from a plain text, or indexed file (.csi,.tsi).
  Only available for nucleotide alignments, and requires at least one sequence to have known genomic coordinates.
- 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.