From bronze!sol.ctr.columbia.edu!zaphod.mps.ohio-state.edu!uwm.edu!ux1.cso.uiuc.edu!phylo!smith Sat Apr 25 10:18:50 EST 1992 Article: 2388 of bionet.software Newsgroups: bionet.software Path: bronze!sol.ctr.columbia.edu!zaphod.mps.ohio-state.edu!uwm.edu!ux1.cso.uiuc.edu!phylo!smith From: smith@phylo.life.uiuc.edu (Steven Smith) Subject: GDE2.0 Now available Message-ID: Sender: usenet@ux1.cso.uiuc.edu (News) Organization: University of Illinois at Urbana Date: Sat, 25 Apr 1992 14:55:11 GMT Lines: 57 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@nucleus.harvard.edu