PC SequenceAnalysis Software wanted
magoldst at ix.netcom.com
Mon Jul 29 16:55:46 EST 1996
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.
gilbertd at bio.indiana.edu (Don Gilbert) wrote:
>SeqPup is a free sequence analysis package that may be of interest.
>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.
> + 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
>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
More information about the Bio-soft