PC SequenceAnalysis Software wanted
jquinn at nntp.best.com
Mon Jul 29 00:11:26 EST 1996
I have been checking out this package recently and I too would strongly
advise trying it out, particularly if you have access to GCG with a 'BOP'
server running; I use it both at home and work now and have found it to be
a most useful (and sufficiently stable) interface to my favorite seq
analysis software (both freeware and GCG).
Don Gilbert (gilbertd at bio.indiana.edu) wrote:
: SeqPup is a free sequence analysis package that may be of interest.
: -= Don
: SeqPup, version 0.6 development release, June/July 1996
: New in this release:
: Easily use GCG and other command-line software over network
: Bare-bones autosequencer (ABI,SCF) base calling, editing, assembly
: Expanded sequence size limits (now can open 1.9MB H.flu genome)
: Numerous bug fixes and improvements
: SeqPup is a biological sequence editor and analysis program
: usable on the common computer systems of Macintosh,
: MS-Windows and X-Windows. It includes links to network
: services and external analysis programs.
: Features include
: + multiple sequence alignment and single sequence editors
: - read and write several sequence file formats
: + easy hand alignment features including colored bases and sliding
: * Internet sequence analysis services by BOP and email methods
: - automatic multiple sequence alignment with ClustalW app
: - automatic gel fragment alignment to contigs with CAP app
: * automatic base calling from ABI or SCF trace files with autoseq app
: - phylogenetic analysis of alignments with fastDNAml and LSADT apps
: - consensus, reverse, complement, degap, and distance/similarity operations
: - restriction maps
: + pretty print of alignments and sequences with boxed and shaded regions.
: - translate dna to/from protein using various codon tables
: + find strings and ORFs
: - automatic preference saving
: - user-definable links to external analysis programs
: (* new, + updated)
: NOTICE: This release is still unfinish, and has bugs. It may
: be useful to you as is, but be warned that it is still prone
: to problems.
: You can obtain this release thru anonymous ftp, gopher or
: http to iubio.bio.indiana.edu, in folder /molbio/seqpup.
: Versions are available for Macintosh (PowerMac and 68K),
: MS Windows (Win95, WinNT and Win3), and Unix/XWindows systems
: including Sun Solaris, SGI Irix, DEC Unix, Linux. The Internet
: locators to this software are
: -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu
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