PC SequenceAnalysis Software wanted

[Marc Goldstein]

Hi Don,

	Thanks for your response to my question, and thanks to others who have
answered so far. I have downloaded and am still playing with Seqpup.
It looks like an impressive piece of work for a free package. The only
problem I have is that I am looking for STAND ALONE software that I
can use when I am not network-connected. I like SeqPup so far, and
will probably find use for many of its features. But I would LOVE it
if the multiple sequence alignment function was part of the program
rather than an interface to a network server... I haven't gotten any
of the network stuff running yet; quite possibly because I use
NetCruiser software for my internet connection, rather than the
standard Trumpet or some such. I'll have fun playing around with it.

	But thanks for your response, and thanks for a lot of hard work in the
development of SeqPup. To those out there with a constant network
connection, you should definitely look into this package.

Marc 


gilbertd at bio.indiana.edu (Don Gilbert) 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