PC SequenceAnalysis Software wanted

Don Gilbert gilbertd at bio.indiana.edu
Sat Jul 27 19:58:41 EST 1996


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




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