Mulitple alignment editor

Michael A. Lonetto lonetto at CGL.UCSF.EDU
Wed Oct 30 13:52:32 EST 1996

>Kay Hofmann wrote:
>> Francois Jeanmougin (pingouin at crystal.u-strasbg.fr) wrote:
>> :       You can easily integrate this editor in your environment using
>> : the app-default file (or your .Xdefault) with lines like:
>> : Seaview*save:                   clustal
>> :       It is written in the help...
>> :                                       Francois.
>ok. It does look neat but the reason why I am staying with GDE
>at the moment is
>b) I could not persuade seaview to chop the ends of an alignment
>(the natural way is... highlight it and 'cut' or something similar).
>Is there some way to do this. This is the second most common use
>of a multiple alignment editor for me (the first being the actual

I agree.  There is a slightly roundabout, but OK way of doing  this
in seaview.  You have to invoke the "sites" selection and then
save the selected sites.  Not as simple as trimming the ends, but
more general (you can also cut out nonconserved insertions
within the alignment).


1) Sites menu:create set.  Give it a name if desired.
2) click and drag in the bottom line that appears (white
dashes to start.)  Wherever you click or drag though
the dashes turn to X's.  These are your sites.
3) File menu:Save Current Sites

that's it.


Michael Lonetto ** 415-476-1493 ** lonetto at cgl.ucsf.edu
UCSF Depts. of Stomatology and Micro.,San Francisco,CA 94143-0512
=-=-=-=-=-=-=----- http://terminator.ucsf.edu/ -----=-=-=-=-=-=-=

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