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.
- Neighbour Joining Using PAM250
- Neighbour Joining Using Sequence
Feature Similarity
- Neighbour Joining Using Blosum62
- Neighbour Joining Using % Identity
- Average Distance Using PAM250
- Average Distance Using Sequence
Feature Similarity
- Average Distance Using Blosum62
- Average Distance Using % Identity
- 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 similarity scores calculated over 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.
- Translate as cDNA (not applet)
This option is visible for nucleotide alignments.
Selecting this option shows the DNA's calculated protein product in a new split frame window. Note that the
translation is not frame- or intron-aware; it simply translates all codons in each sequence, using the
standard genetic code (any incomplete final codon is discarded).
You can perform this action on the whole alignment,
or selected rows, columns, or regions.
- Get Cross-References (not applet)
This option is visible where sequences have cross-references to
other standard databases; for example, an EMBL entry may have cross-references to one or more UNIPROT entries.
Select the database to view all cross-referenced sequences in a new split frame window.
- 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.
- Show Flanking Regions
Opens
a new alignment window showing any additional sequence data
either side of the current alignment. Useful in conjunction with
'Fetch Database References' when the 'Trim Retrieved Sequences'
option is disabled to retrieve full length sequences for a set
of aligned peptides.