Alignment Window Calculate Menu
- By ID
This will sort
the sequences according to sequence name. If the sort is
repeated, the order of the sorted sequences will be
- By Length
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
will sort the sequences according to sequence name. If the
sort is repeated, the order of the sorted sequences will be
- 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
- Calculate Tree or PCA ...
calculations dialog for
for calculating trees or
principal component analysis
plots on the alignment or the currently selected
- Pairwise Alignments
Smith and Waterman algorithm to selected sequences. See pairwise
- Extract Scores ... (optional)
option is only visible if Jalview detects one or more
white-space separated values in the description line of the
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
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. You can use the standard genetic code, or choose an
alternative code table (any incomplete final codon is discarded).
You can perform this action on the whole alignment, or selected
rows, columns, or regions. Alternative code tables were added in
- Reverse, Reverse Complement (not applet)
These options are visible for nucleotide alignments.
Selecting them adds the reverse (or reverse complement) of the
sequences (or selected region) as new sequences in the
alignment. To try this out, add this sequence and perform
'Reverse Complement' followed by 'Translate as cDNA':
- 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
- Autocalculate Consensus
large alignments it can be useful to deselect
"Autocalculate Consensus" when editing. This prevents
the sometimes lengthy calculations performed after each sequence
- Sort Alignment With New Tree
this option is selected, the alignment will be automatically
sorted whenever a new tree is calculated or loaded.
- Show Flanking Regions
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.