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 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 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.
  
• Autocalculate Consensus
  For large alignments it can be useful to deselect "Autocalculate Consensus" when editing. This prevents lengthy calculations which are performed after each sequence edit.