In article <9302191505.AA16497 at net.bio.net> Dave Knecht,
KNECHT at UCONNVM.bitnet writes:
>I seemed to have idadvertantly touched a nerve- I really did not intend
to fla
>me GCG. I agree that it is the best and most comprehensive package
available a
>nd I use it. I find that 95% of what I do, I can do on my Mac with
shareware p
>lus DNA Strider. The other 5% I do on GCG with a manual on my map
because I ca
>nnot remember form one time to the next what the commands are.
I too think that using a hybrid approach seems to make the most sense
right now. Especially for those with internet access. On the mac:
(1) assembling with sequencher is straightforward
(and sequencher can read and write in many formats),
(2) analyze with intron/exon guessers like GRAIL (by email server)
(3) search with BLAST (by email server)
(4) retrieve sequences (using the retrieve email server)
(all of these things can be done from Gilbert's seqApp or with
Eudora as an email mac front end)
(5) multiple alignment using clustalV (also possible from seqApp,
but it might be nice to find other ways to do this)
(note that superClock is not compatible with seqApp's implementation of
Clustal V)
(note that superClock is not compatible with
seqApp's implementation of Clustal V)
(6) work on the multiple alignment in MacPaup (from Swofford)
(7) play with and construct your trees in MacClade (from Sinaur)
(7b) look at MacT
etc...
Note that any parts of this that you want to do with another tool you can.
Much of this will be even easier to recommend once seqApp pulls out of
alpha and into a more stable versions.
I am interested to hear if there are folks who find this patchwork
approach problematic (and to hear what other programs are part of your
patchwork).
I do think that it can be a bit of a support
problem since you can't just hand someone a 20 lb GCG manual and hope that
they don't come back.
Jeremy John Ahouse
Center for Complex Systems and Biology Dept
Brandeis University
Waltham, MA 02254-9110
(617) 736-4954
email: ahouse at hydra.rose.brandeis.edu
