PC SequenceAnalysis Software wanted

Greg 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
: 	
: Summary

: 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

:   <ftp://iubio.bio.indiana.edu/molbio/seqpup/>
:   <gopher://iubio.bio.indiana.edu/11/IUBio-Software+Data/molbio/seqpup/>
:   <http://iubio.bio.indiana.edu/1/IUBio-Software%2bData/molbio/seqpup/>

: --
: -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu




More information about the Bio-soft mailing list