Five output formats are offered. You can choose more than one (or all 5 if
CLUSTAL format output is a self explanatory alignment format. It shows the
sequences aligned in blocks. It can be read in again at a later date to
(for example) calculate a phylogenetic tree or add a new sequence with a
GCG output can be used by any of the GCG or EGCG programs that can work on multiple
alignments (e.g. PRETTY,
PLOTALIGN). It is the same as the GCG
.msf format files (multiple sequence file); new in version 7 of GCG.
PHYLIP format output can be used for input to the PHYLIP package of Joe
Felsenstein. This is an extremely widely used package for doing every
imaginable form of phylogenetic analysis (MUCH more than the the modest intro-
duction offered by this program).
NBRF/PIR: this is the same as the standard PIR format with ONE ADDITION. Gap
characters "-" are used to indicate the positions of gaps in the multiple
alignment. These files can be re-used as input in any part of clustal that
allows sequences (or alignments or profiles) to be read in.
GDE: this format is used by the GDE package of Steven Smith.
OUTPUT ORDER is used to control the order of the sequences in the output
alignments. By default, it is the same as the input order. This switch can
be used to make the order correspond to the order in which the sequences
were aligned (from the guide tree/dendrogram), thus automatically grouping
closely related sequences.