If you have already loaded sequences, use menu item 1
to do the complete
multiple alignment. You will be prompted for 2 output files: 1 for the
alignment itself; another to store a dendrogram that describes the similarity
of the sequences to each other.
Multiple alignments are carried out in 3 stages (automatically done from menu
item 1 ...Do complete multiple alignments now):
- all sequences are compared to each other (pairwise alignments);
- a dendrogram (like a phylogenetic tree) is constructed, describing the
approximate groupings of the sequences by similarity (stored in a file).
- the final multiple alignment is carried out, using the dendrogram as a guide.
parameters control the speed/sensitivity of the initial
parameters control the gaps in the final multiple alignments.
(menu item 7)
will remove any new gaps introduced into the sequences
during multiple alignment if you wish to change the parameters and try again.
This only takes effect just before you do a second multiple alignment. You
can make phylogenetic trees after alignment whether or not this is ON.
If you turn this OFF, the new gaps are kept even if you do a second multiple
alignment. This allows you to iterate the alignment gradually. Sometimes, the
alignment is improved by a second or third pass.
(menu item 8)
can be used to send the output alignments to the screen
as well as to the output file.
You can skip the first stages (pairwise alignments; dendrogram) by using an
old dendrogram file (menu item 3);
or you can just produce the dendrogram
with no final multiple alignment (menu item 2).
: Menu item 9 (format options) allows you to choose from 5
different alignment formats (CLUSTAL, GCG, NBRF/PIR, PHYLIP and GDE).