Alignment Window Calculate Menu

- Sort
  - by ID
    This will sort the sequences according to sequence name. If the sort is repeated, the order of the sorted sequences will be inverted.
  - by Length
    This will sort the sequences according to their length (excluding gap characters). If the sort is repeated, the order of the sorted sequences will be inverted.
  - by Group
    This will sort the sequences according to sequence name. If the sort is repeated, the order of the sorted sequences will be inverted.
  - by Pairwise Identity
    This will sort the selected sequences by their percentage identity to the consensus sequence. The most similar sequence is put at the top.
  - The Sort menu will have some additional options if the alignment has any associated score annotation, or you have just done a multiple alignment calculation or opened a tree viewer window.
- Calculate Tree
  Functions for calculating trees on the alignment or the currently selected region. See calculating trees.
  - Average Distance Using % Identity
  - Neighbour Joining Using % Identity
  - Average Distance Using Blosum62
  - Neighbour Joining Using Blosum62
- Pairwise Alignments
  Applies Smith and Waterman algorithm to selected sequences. See pairwise alignments.
- Principal Component Analysis
  Shows a spatial clustering of the sequences based on the BLOSUM62 scores in the alignment. See Principal Component Analysis.
- Extract Scores ... (optional)
  This option is only visible if Jalview detects one or more white-space separated values in the description line of the alignment sequences.
  When selected, these numbers are parsed into sequence associated annotation which can then be used to sort the alignment via the Sort by→Score menu.
- Autocalculate Consensus
  For large alignments it can be useful to deselect "Autocalculate Consensus" when editing. This prevents the sometimes lengthy calculations performed after each sequence edit.
- Sort Alignment With New Tree
  If this option is selected, the alignment will be automatically sorted whenever a new tree is calculated or loaded.