Multiple alignments

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):
  1. all sequences are compared to each other (pairwise alignments);
  2. a dendrogram (like a phylogenetic tree) is constructed, describing the approximate groupings of the sequences by similarity (stored in a file).
  3. the final multiple alignment is carried out, using the dendrogram as a guide.

PAIRWISE ALIGNMENT parameters control the speed/sensitivity of the initial alignments.

MULTIPLE ALIGNMENT parameters control the gaps in the final multiple alignments.

RESET GAPS (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.

SCREEN DISPLAY (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).

OUTPUT FORMAT : Menu item 9 (format options) allows you to choose from 5 different alignment formats (CLUSTAL, GCG, NBRF/PIR, PHYLIP and GDE).