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.