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.
GDE OUTPUT CASE: sequences in GDE format may be written in either upper or
CLUSTALW SEQUENCE NUMBERS: residue numbers may be added to the end of the
alignment lines in clustalw format.
OUTPUT ORDER is used to control the order of the sequences in the output
alignments. By default, the order corresponds to the order in which the
sequences were aligned (from the guide tree/dendrogram), thus automatically
grouping closely related sequences. This switch can be used to set the order
to the same as the input file.
PARAMETER OUTPUT: This option allows you to save all your parameter settings
in a parameter file. This file can be used subsequently to rerun ClustalW
using the same parameters.