[BiO BB] Sequence Editor for Unix?

Maximilian Haeussler maximilianh at gmail.com
Fri Feb 3 09:51:19 EST 2006


in 2000 and 2002 someone asked on this list if there was a good
replacement for the Bioedit sequence editor for Unix. Some time has
passed from this.

So I'm asking the question again:
What are you using as a sequence editor on Linux if you have a
Biologist standing next to who who'd like to see a graphical view of
the alignment of a couple of sequences in Blast, Clustal, etc? Bioedit
could do all of this easily and quickly without any hassles.

I've tried a couple of programs. Personally, I don't like java
swing...interfaces feel rather sluggish. Apollo/Artemis take ages to
load if you just want to have a look on an alignment or run a Blast.
Strap has a strange interface. Seqpup hasn't been updated for years.
Clustalx is OK for alignment viewing can only run ClustalW.

Maybe just a small executable, C-style, that can plot blast/gff-files
and zoom, might be sufficient...

What are you using?

Thanks a lot,

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