From: mangalam@SALK-SC2.SDSC.EDU
Newsgroups: bionet.software
Subject: Reviews of Seq Analysis Progs (longish)
Date: 8 Sep 92 23:18:28 GMT
Distribution: bionet



Harry Mangalam                                   Vox:(619) 453-4100, x250
Dept of Biocomputing                                   Fax:(619) 552-1546
The Salk Institute                             mangalam@salk-sc2.sdsc.edu
10010 N Torrey Pines Rd                        mangalam@salk-sgi.sdsc.edu
La Jolla CA 92037                                    mangalam@salk.bitnet
Greetings, Netlandos,

   In response to the recent spate of advisories, queries, and warnings
about sequence analysis programs (SAPs), I thought I'd muddy the metaphoric
waters further by throwing my own $.02 into the ring.

   I work in a mostly Mac environment hence the emphasis is on Mac
software.  A few PC packages are included mostly because they are useful
enough to warrant putting up with the hassle of transferring and modifying
files.  I have recently begun to work in an X window situation and
therefore a few X Window programs are also included.  Notably absent from
this review is Steve Smith's Genetic Data Environment (GDE), but I will try
to get to it Real Soon Now.  It is, for those who don't know, an
extensible, X window app for molecular biology whose server program
(client, in the bizzarro world of X) runs on a Sun SPARC hardware (and now
on SGI, thanks to Anthony Persechini).  But enough of GDE for now.

   If you're looking for a program that will do everything from restriction
maps to multiple alignments, will make only a polite dent in your wallet,
is well-debugged, takes advantage of the latest network services, co-exists
peacefully with the rest of your applications and is easy to use, you will
have to search beyond the narrow confines of this planet.  
   Many of the packages mentioned below are commercially produced and thus
have to make a profit. Because of the restricted market for sales (as
opposed to a general purpose package like a spreadsheet or word processor),
they must be relatively expensive and many address the all-too-common
practice of software piracy by requiring the presence of a hardware lock. 
Those that are freeware obviously cannot support the level of debugging and
support of a commercial program, however there are some that are of
surprisingly high quality.  

   The following notes are not meant as an exhaustive, objective review. 
They are my opinions (and a few measurements) based on having used the
programs or the demo versions and are obviously biased by my approach to
various problems - what I may dismiss without a thought may be a critical
determinant for someone else.  And certainly, don't take my word for it -
I've (fitfully) tried to include the email addresses of people who have
taken opposing views.  Also, while I have made a reasonable attempt to be
accurate, features, updates, and prices change so often in this field that
like many reviews, this one is sliding into obsolescence as you read it. 
All prices are approximate (and sometimes negotiable, especially at the end
of a fiscal period).
   Consider this a work in progress - as time allows, I plan to post
reviews of other packages not covered here and increase the detail of the
reviews, but for now a quick overview will have to do.  I invite comments,
corrections, and flames and will certainly post explanations, expansions,
apologies, and retractions if they are warranted.


Additional Sources of Information on SAPs:
  You can also search the archived biosci postings for additional
information by WAIS and gopher.  One gopher path is: 

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