Alignment Menu

• File
• 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 output maintaining the 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 coloursof 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 load in trees which are in the Newick file format and associate them with a particular alignment. Note: the ids of the tree file and your alignment MUST be the same.
• Close
  Close the alignment window. Be aware that changes to your alignment will not be save unless specifically actioned from the "Save As" menu.
  
• Edit

• Undo
  This will undo any edits you make to the alignment. This applies to insertion or deletion of gaps, cutting residues or sequences from the alignment, pasting
• Redo
  
• Cut
• Copy
• Paste
  • To New Alignment
  • Add To This Alignment
• Delete
• Select All
• Deselect All
• Invert Selection
• Undefine Groups
• Remove Left
• Remove Right
• Remove Empty Columns
• Remove All Gaps
• Remove Redundancy
• Pad Gaps

• Search

• Find

• View

• Font
• Wrap
• Show Full Sequence ID
• Boxes
• Text
• Colour Text
• Show Gaps
• Show Annotations
• Sequence Features
• Overview Window

• Colour

• Apply Colour To All Groups
• None
• ClustalX
• Blosum62 Score
• Percentage Identity
• Zappo
• Taylor
• Hydrophobicity
• Helix Propensity
• Strand Propensity
• Turn Propensity
• Buried Index
• Nucleotide
• User Defined
• By Conservation
• Modify Conservation Threshold
• Above Identity Threshold
• Modify Identity Threshold

• Calculate

• Sort
  • by ID
  • by Group
  • by Pairwise Identity
• Calculate Tree
  • Average Distance Using % Identity
  • Neighbour Joining Using % Identity
  • Average Distance Using Blosum62
  • Neighbour Joining Using Blosum62
• Paiwise Alignments
• Principal Component Analysis
• Web Service
  • Clustal Alignment
  • JPred
  • Muscle Alignment