The second release of GDE is now available via anonymous ftp to
golgi.harvard.edu (128.103.161.61). The current distribution is
Sun4 (Sparcstation) binaries. The source code release will follow
shortly as well as the Decstation version.
New features for this release include:
Improved sequence editing functions
Support for contig Assembly
Restriction map analysis
Access to homology searching
Additional phylogenetic support
Secondary Structure prediction
Access to Email services
This release includes program contributions from:
Des Higgins
David Lipman and the group at NCBI
William Pearson
Don Gilbert
Xiaoqui Huang
Joe Felsenstein
Michael Zuker
Geert DeSoete
Michael Maciukenas and the group at the Ribosomal Database Project
The GDE is a analysis tool designed primarily for nucleic and amino acid
sequence analysis. The GDE currently runs on SUN SparcStations using
OpenWindows 2.0 or MIT X11R4. The programs use an expandable user interface
which allows the addition of external analysis functions without any rewriting
of code. Analysis functions can be written in any language ('C',Fortran,
Pascal Basic, shell scripts), and can be seamlessly merged into the systems
menu/dialog box interface.
The system supports several data types, nucleic and amino acid sequences,
text, and masking sequence, and three forms of color highlighting. The system
can handle enormous alignments limited only by the amount of virtual memory
on your workstation.
Sequences can be edited under several levels of protection, as well
as by aligned groups. The system has several external analysis
functions included for such things as automated alignment, searching,
homology recognition, and phylogenetic analysis.
The programs are not in the public domain, but are and will continue to be
available for free. Distribution will includes full source code, and binaries
along with a users manual.
Steven Smith
Director of Computation
Harvard Genome Lab
smith at nucleus.harvard.edu
