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Summary

SeqPup is a biological sequence editor and analysis program usable on the common computer systems including Macintosh, MS-Windows and X-Windows. It includes links to network services and external analysis programs.

Features include

+ multiple sequence alignment and single sequence editing

read and write several sequence file formats

+ easy hand alignment features including colored bases and sliding

* Internet sequence analysis services (e.g, GCG) by BOP and email methods

* automatic base calling from ABI or SCF trace files with autoseq app

automatic multiple sequence alignment with ClustalW app

automatic gel fragment alignment to contigs with CAP app

phylogenetic analysis of alignments with fastDNAml and LSADT apps

phylogenetic tree drawing with DrawTree and DrawGram Phylip 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.

SeqPup is being written using DCLAP, a free and portable C++ class application framework. DCLAP is founded on the NCBI Toolkit, especially it's Vibrant user-interface section written primarily by Jonathan Kans. SeqApp/SeqPup was started in 1990 as sequence editor/analysis platform on which analysis programs from other authors could be easily incorporated into a useable interface.

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/>

Source code for this software is at <ftp://iubio.bio.indiana.edu/util/dclap/source/>.

The bopper source for installed a server for SeqPup Internet BOP functions is in this same folder as <ftp://iubio.bio.indiana.edu/util/dclap/source/bopper.tar.gz>

Comments, bug reports and suggestions for new features are very welcome and should be sent via e-mail to <mailto://SeqPup@Bio.Indiana.Edu/>.

June/July 96: version 0.6d release

+ "bopper" Internet protocol for client/server use of command line programs such as the GCG suite.

+ autoseq base calling app for reading ABI and SCF sequencer trace file data, plus base/trace editing functions.

+ Started expanding maximum sequence limit to 2 megabases (from about 30Kb), however most functions beyond viewing will still fail for >30Kb sequences.

+ Several bug fixes are included for mac, mswin, unix. Added background color in align view, minimum ORF size pref, improved tracking of changed data, improved align editing, save pretty print to PICT or text; fixed child app bugs; fixed mswin edit truncation to 255 bases; editable data tables in selection dialogs


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