P.S. on SeqPup usage to delete columns.
You can use it now to do what you want, using the current mask
functions. If you create a mask that includes only the
data of interest to you, then you can choose the Sequence/Seq Masks/
Compress by mask command. This will eliminate all but the masked
To create the mask that you need, in the multi align view, select
the "View" popup menu to point to Mask # 1, 2, 3 or 4. A short hand
for selecting full columns of bases is to click the column index
line above the bases. Hold mouse down and select many columns.
If your bad subset is smaller than your good subset, select the
bad subset, then choose the Sequence/Seq Masks/Invert mask function
to select the good subset. Save the data now to have your mask
persist to the next session. Then do the above 'Compress by mask'
and analyze that good data subset.
You can also use masks to specify non-contiguous, irregular subsets
of data, rather than just columns, if that is of interest.
PPS, I know a better manual is needed so one can figure out things
-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu