UNIX SOFTWARE
EBI
Hinxton, Hinxton Hall,
Cambridge CB10 1RQ,
United Kingdom
E-mail: SOFTWARE@ebi.ac.uk
File: GDE1_0.tar.Z.
Update: 1-Jul-1991.
Version: 1.0.
Size:
280 k
Compressed: TAR,.
Author:
Harvard Genome Lab
Description:
Expandable set of programs for multiple sequence
alignment and analysis (binaries)
Literature:
-
Source Code:
-
SW Requirements:
OpenWindows 2.0 or MIT X11R4
HW Requirements:
SUN SparcStation
File: GDE_Doc.tar.Z.
Update: 1-Jul-1991.
Version: 1.0.
Size:
400 k
Compressed: TAR,.
Author:
Harvard Genome Lab
Description:
Expandable set of programs for multiple sequence
alignment and analysis (documentation - Postscript)
Literature:
-
Source Code:
-
SW Requirements:
-
HW Requirements:
-
File: GDE_src.tar.Z.
Update: 1-Jul-1991.
Version: 1.0.
Size:
290 k
Compressed: TAR,.
Author:
Harvard Genome Lab
Description:
Expandable set of programs for multiple sequence
alignment and analysis (source code)
Literature:
-
Source Code:
-
SW Requirements:
OpenWindows 2.0 or MIT X11R4
HW Requirements:
SUN SparcStation
File: ShadyBox.tar.Z.
Update: 1-Jun-1994.
Version: 1.0.
Size:
5.7 M
Compressed: TAR,.
Author:
C. Huynh
Description:
Pretty plots of multiple alignments
Literature:
-
Source Code:
C
SW Requirements:
X-Windows
HW Requirements:
-
File: blast.tar.Z.
Update: 15-Jun-1992.
Version: -.
Size:
330 k
Compressed: TAR,.
Author:
Myers E.W., Miller W., Altschul S.F., Gish W. and
Lipman, D.J.
Description:
Fast sequence database searching.
Literature:
J. Mol. Biol. 215 (1990), 403-410
Source Code:
C
SW Requirements:
Files DFA, GISH and NCBI are required!
HW Requirements:
-
File: blocksearch.tar.Z.
Update: 6-Dec-1993.
Version: 2.1.
Size:
45 k
Compressed: TAR,COMPRESS.
Author:
Fuchs R.
Description:
Functional analysis of protein sequences with
scoring matrices derived from the BLOCKS database
Literature:
CABIOS 9 (1993), 587-591
Source Code:
C
SW Requirements:
-
HW Requirements:
-
File: box_exe_axposf1.tar.Z.
Update: 27-May-1994.
Version: 2.7.
Size:
360 k
Compressed: TAR,COMPRESS.
Author:
Hofmann K.
Description:
Pretty display of multiply aligned sequences
Literature:
-
Source Code:
-
SW Requirements:
-
HW Requirements:
Alpha/AXP
File: btab.tar.Z.
Update: 22-Dec-1992.
Version: -.
Size:
170 k
Compressed: TAR,.
Author:
Dubnick M.
Description:
BLAST output parser
Literature:
CABIOS 8 (1992), 601-602
Source Code:
C, yacc, lex
SW Requirements:
-
HW Requirements:
-
File: clustalv.tar.Z.
Update: 8-Aug-1991.
Version: 5.
Size:
90 k
Compressed: TAR,.
Author:
Higgins D., Fuchs R. and Bleasby A.J.
Description:
Multiple sequence alignment
Literature:
CABIOS 8 (1992), 189-191
Source Code:
C
SW Requirements:
ANSI C compiler or GNU C compiler
HW Requirements:
-
File: cregex.c.
Update: 7-Oct-1992.
Version: 1.2.
Size:
15 k
Compressed: -.
Author:
Leunissen J.
Description:
Reformating of Prosite for use with Kolakowski's PROSEARCH
Literature:
-
Source Code:
C
SW Requirements:
(used by PROSEARCH [prosearch.tar.Z])
HW Requirements:
-
File: dbget.tar.Z.
Update: 28-Apr-1994.
Version: 1.2.
Size:
20 k
Compressed: TAR,COMPRESS.
Author:
Fuchs R.
Description:
Utility for downloading database entries from mail servers
Literature:
-
Source Code:
C
SW Requirements:
-
HW Requirements:
-
File: dfa.tar.Z.
Update: 15-Jun-1992.
Version: -.
Size:
80 k
Compressed: TAR,.
Author:
Gish W.
Description:
Routines for finite state automaton used by BLAST
Literature:
J. Mol. Biol. 215 (1990), 403-410
Source Code:
C
SW Requirements:
-
HW Requirements:
-
File: double-digester.tar.Z.
Update: 24-Mar-1993.
Version: 1.1b.
Size:
5.3 MB
Compressed: TAR,.
Author:
Wright L.
Description:
Graphical analysis of double digest restriction data
Literature:
-
Source Code:
-
SW Requirements:
X11
HW Requirements:
SUN SPARCstation
File: dtask11s.tar.Z.
Update: 26-Apr-1993.
Version: 1.1s.
Size:
306 k
Compressed: TAR,.
Author:
Hauge G.E.
Description:
Smith-Waterman database searches on parallel workstations
Literature:
-
Source Code:
C
SW Requirements:
BSD or SysV with BSD signals
HW Requirements:
-
File: filter.tar.Z.
Update: 16-Dec-1992.
Version: -.
Size:
80 k
Compressed: TAR,COMPRESS.
Author:
Argos, P., Vingron, M., Rechid, R. and McCaldon, P.
Description:
Set of programs for suboptimal alignments and recognition
of reliably aligned regions in protein sequence
comparisons and to multiply align and find conserved
motifs from a set of sequences
Literature:
Protein Eng. 3 (1990), 565-569
J.Mol.Biol. 218 (1991), 33-43
Source Code:
C
SW Requirements:
-
HW Requirements:
SUN 2,3 or 4
File: gci.tar.Z.
Update: 25-May-1992.
Version: 1.0.
Size:
80 k
Compressed: TAR,.
Author:
Tuparev G., Vriend, G. and Sander C.
Description:
A network server for interactive 3D graphics
Literature:
J. Mol. Graphics 10 (1992), 12-16
Source Code:
C
SW Requirements:
-
HW Requirements:
Silicon Graphics IRIS workstation
File: genal.tar.Z.
Update: 7-Mar-1994.
Version: 2.0.
Size:
55 k
Compressed: TAR,.
Author:
Stoevlbaek J.
Description:
Alignments of genomic sequences with coding regions
Literature:
-
Source Code:
C
SW Requirements:
-
HW Requirements:
-
File: gish.tar.Z.
Update: 15-Jun-1992.
Version: -.
Size:
25 k
Compressed: TAR,.
Author:
Gish W.
Description:
Auxilliary routines for BLAST
Literature:
J. Mol. Biol. 215 (1990), 403-410
Source Code:
C
SW Requirements:
-
HW Requirements:
-
File: gm.tar.Z.
Update: 10-May-1993.
Version: 2.0.
Size:
540 k
Compressed: TAR,.
Author:
Fields C.A. and Soderlund C.A.
Description:
Analysis of unknown DNA sequences
Literature:
CABIOS 6 (1990), 263-270
Source Code:
C
SW Requirements:
-
HW Requirements:
-
File: gmd.txt.
Update: 22-Jan-1992.
Version: -.
Size:
25 k
Compressed: -.
Author:
Fu Y. and Arnold J.
Description:
Programs to assist in the design of genome mapping
experiments (contig mapping)
Literature:
Biometrics, in press
Source Code:
Fortran
SW Requirements:
Fortran compiler for recompilation
HW Requirements:
-
File: homochart.tar.Z.
Update: 3-Apr-1991.
Version: -.
Size:
8 k
Compressed: TAR,.
Author:
Smith R.
Description:
Plotting multiple sequence alignments with boxes around
identical residues
Literature:
-
Source Code:
C
SW Requirements:
-
HW Requirements:
-
File: hth.c.
Update: 4-Jan-1994.
Version: 1.0.5.
Size:
10 k
Compressed: -.
Author:
Halling C.
Description:
Prediction of helix-turn-helix regions in protein sequences
Literature:
-
Source Code:
C
SW Requirements:
-
HW Requirements:
-
File: icatools.tar.Z.
Update: 24-Nov-1992.
Version: 1.1.
Size:
240 k
Compressed: TAR,COMPRESS.
Author:
Parsons J.
Description:
Clustering and statistical analysis of large cDNA
collections
Literature:
CABIOS 8 (1992), 461-466
Source Code:
C
SW Requirements:
-
HW Requirements:
-
File: icrf_contig.tar.Z.
Update: 29-Oct-1992.
Version: 1.
Size:
450 k
Compressed: TAR,COMPRESS.
Author:
Mott R.F. and Grigoriev A.V.
Description:
Software tools for ordering clone libraries based on
hybridisation data
Literature:
Nucleic Acids Res., submitted
Source Code:
C
SW Requirements:
SUN XVIEW libraries
HW Requirements:
SUN
File: issc.tar.Z.
Update: 7-Oct-1992.
Version: -.
Size:
460 k
Compressed: TAR,COMPRESS.
Author:
Argos, P., Vingron, M., Rechid, R. and McCaldon, P.
Description:
Sensitive sequence comparison package including
graphics program for visualisation and interaction with
dotmatrices
Literature:
J. Mol. Biol. 193 (1987), 385-396
CABIOS 5 (1989), 107-113
Source Code:
C, Fortran
SW Requirements:
-
HW Requirements:
SUN 2,3 or 4
File: mailfasta.shar.
Update: 5-Aug-1993.
Version: 3.2.
Size:
45 k
Compressed: TAR,.
Author:
deBoer T.
Description:
Script for using EMBL/GenBank Mail-FASTA servers
Literature:
-
Source Code:
C, csh
SW Requirements:
readseq.tar.Z
HW Requirements:
-
File: mase.tar.Z.
Update: 30-Jul-1990.
Version: -.
Size:
685 k
Compressed: TAR,.
Author:
Faulkner D. V.
Description:
Multiple sequence editor
Literature:
TIBS 13 (1989), 321-322
Source Code:
C
SW Requirements:
-
HW Requirements:
-
File: menugcg.uue.
Update: 30-Aug-1993.
Version: 5.2.
Size:
20 k
Compressed: TAR,.
Author:
Colet M.
Description:
Menu interface to GCG package
Literature:
-
Source Code:
csh script
SW Requirements:
GCG software
HW Requirements:
-
File: molbio.tar.Z.
Update: 11-May-1993.
Version: -.
Size:
540 k
Compressed: TAR,.
Author:
Robison K.
Description:
C++ class library for molecular biology
Literature:
-
Source Code:
C++
SW Requirements:
-
HW Requirements:
-
File: msu.tar.Z.
Update: 6-Apr-1994.
Version: 1.4.
Size:
60 k
Compressed: TAR,COMPRESS.
Author:
Fuchs R.
Description:
Configurable utility for accessing electronic mail servers
Literature:
CABIOS, in press
Source Code:
C
SW Requirements:
-
HW Requirements:
-
File: ncbi.tar.Z.
Update: 15-Jun-1992.
Version: -.
Size:
45 k
Compressed: TAR,.
Author:
Gish W.
Description:
General purpose routines used by BLAST
Literature:
J. Mol. Biol. 215 (1990), 403-410
Source Code:
C
SW Requirements:
-
HW Requirements:
-
File: nseqtool.tar.Z.
Update: 31-Jul-1991.
Version: -.
Size:
250 k
Compressed: TAR,.
Author:
Schnobel R.
Description:
Integrated display of aligned amino acid sequences
and protein structures
Literature:
CABIOS 7 (1991), 341-346
Source Code:
C
SW Requirements:
SunView
HW Requirements:
SUN 4 or SPARCstation, colour graphics display
File: overseer.tar.Z.
Update: 26-Oct-1992.
Version: 1.1.
Size:
50 k
Compressed: ZOO.
Author:
Sibbald P.
Description:
A package for searching nucleic acid sequence data bases
Literature:
CABIOS 8 (1992), 45-48
Source Code:
Pascal
SW Requirements:
-
HW Requirements:
-
File: pima.tar.Z.
Update: 25-Feb-1992.
Version: 1.22.
Size:
495 k
Compressed: TAR,.
Author:
Smith, R.F. and Smith T.F.
Description:
Pattern-induced multi-sequence alignment program
Literature:
PNAS 87 (1990), 118-122
Source Code:
C
SW Requirements:
-
HW Requirements:
-
File: plsearch.tar.Z.
Update: 23-Feb-1992.
Version: 4.2.
Size:
1710 k
Compressed: TAR,.
Author:
Smith, R.F. and Smith T.F.
Description:
Pattern detection in proteins
Literature:
PNAS 87 (1990), 118-122
Source Code:
C
SW Requirements:
-
HW Requirements:
-
File: profile.tar.Z.
Update: 20-Sep-1993.
Version: 1.0.
Size:
200 k
Compressed: TAR,.
Author:
Thompson J.
Description:
Creation of sequence profiles for use with GCG
ProfileSearch
Literature:
CABIOS, in press
Source Code:
C
SW Requirements:
-
HW Requirements:
-
File: prosearch.tar.Z.
Update: 14-Apr-1992.
Version: 2.0.
Size:
83 k
Compressed: TAR,.
Author:
Kolakowski L. F.
Description:
Pattern searching in proteins using Prosite (incl.
CREGEX.C)
Literature:
-
Source Code:
C
SW Requirements:
Awk
HW Requirements:
-
File: rasmol.tar.Z.
Update: 9-Mar-1993.
Version: 2.3.
Size:
715 k
Compressed: TAR,.
Author:
Sayle R.
Description:
Visualisation of macromolecules using PDB files
Literature:
-
Source Code:
C
SW Requirements:
X Window
HW Requirements:
-
File: readseq.tar.Z.
Update: 12-Dec-1993.
Version: 30-Dec-92.
Size:
75 k
Compressed: TAR,.
Author:
Gilbert D. (mods by Alff-Steinberger A.)
Description:
Sequence format conversion program
Literature:
-
Source Code:
C
SW Requirements:
ANSI C compiler
HW Requirements:
-
File: seqf.tar.Z.
Update: 12-Feb-1991.
Version: -.
Size:
145 k
Compressed: TAR,.
Author:
Davison D. and Kanehisa M.
Description:
Package of programs for searching genetic sequence
libraries.
Literature:
-
Source Code:
Fortran
SW Requirements:
-
HW Requirements:
-
File: seqsee.tar.Z.
Update: 3-May-1994.
Version: 1.2.
Size:
3.1 M
Compressed: TAR,.
Author:
Wishart D.S et al.
Description:
Comprehensive program suite for protein sequence analysis
Literature:
CABIOS 10 (1994), 121-132
Source Code:
C
SW Requirements:
-
HW Requirements:
-
File: sigma.tar.Z.
Update: 3-Nov-1993.
Version: 2.0.
Size:
3.8 k
Compressed: TAR,.
Author:
LANL T-10
Description:
System for integrated genome map assembly
Literature:
-
Source Code:
-
SW Requirements:
Motif
HW Requirements:
Sun SparcStation
File: sigscan.tar.Z.
Update: 20-Jul-1993.
Version: 3.3.
Size:
190 k
Compressed: TAR,.
Author:
Prestridge D. S.
Description:
Signal Scan: a program to identify known eukaryotic
signals in DNA sequences
Literature:
CABIOS 7 (1991), 203-206
Source Code:
C
SW Requirements:
-
HW Requirements:
-
File: signal.tar.Z.
Update: 16-Dec-1993.
Version: -.
Size:
90 k
Compressed: TAR,.
Author:
Colgrove R. C.
Description:
Prediction of signal sequence cleavage site
Literature:
Ph.D. dissertation, UCSF Dept. of Biochem., 1990
Source Code:
C
SW Requirements:
-
HW Requirements:
-
File: sigseq.tar.Z.
Update: 19-Jul-1990.
Version: -.
Size:
15 k
Compressed: TAR,.
Author:
Popowicz A.M.
Description:
Prediction of signal sequence cleavage site
Literature:
CABIOS 4 (1988), 405-406
Source Code:
C
SW Requirements:
-
HW Requirements:
-
File: sim.tar.Z.
Update: 5-May-1992.
Version: April.
Size:
17 k
Compressed: TAR,.
Author:
Huang G. and Miller W.
Description:
Local similarity searching
Literature:
CABIOS 6 (1990), 373 - 381.
Source Code:
C
SW Requirements:
-
HW Requirements:
-
File: status.tar.Z.
Update: 31-Jul-1992.
Version: -.
Size:
203 k
Compressed: TAR,.
Author:
Dubnick M.
Description:
Tools for managing large DNA-sequencing projects
Literature:
CABIOS 8 (1992), 291-292.
Source Code:
C
SW Requirements:
-
HW Requirements:
-
File: super.tar.Z.
Update: 4-Feb-1993.
Version: 2.0.
Size:
95 k
Compressed: TAR,.
Author:
Rosenthaler L. and Doelz R.
Description:
Tool for performing electronic user polls
Literature:
-
Source Code:
C
SW Requirements:
-
HW Requirements:
-
File: tbob.tar.Z.
Update: 30-May-1994.
Version: 3.2.
Size:
35 k
Compressed: TAR,COMPRESS.
Author:
Rioux P.
Description:
BLAST output parser
Literature:
-
Source Code:
Perl
SW Requirements:
Perl
HW Requirements:
-
File: tfd2prosite.c.
Update: 13-Dec-1991.
Version: 1.3.
Size:
10 k
Compressed: -.
Author:
Fuchs R.
Description:
Program to convert SITES and DOMAINS tables of TFD
database to Prosite format.
Literature:
-
Source Code:
C
SW Requirements:
-
HW Requirements:
-
File: tkdcse-sgi-3.0.tar.Z.
Update: 27-May-1994.
Version: 3.0.
Size:
3.5 M
Compressed: TAR,.
Description:
Multiple alignment editor
Literature:
CABIOS, submitted
Source Code:
tcl/tk
SW Requirements:
X-Windows
HW Requirements:
SGI
File: tmap.tar.Z.
Update: 21-April-1994.
Version: 46.
Size:
30 k
Compressed: TAR,.
Description:
Prediction of transmembrane segments in proteins utilising
multiple sequence alignments
Literature:
J. Mol. Biol. 237 (1994) 182-192
Source Code:
C
SW Requirements:
-
HW Requirements:
-
File: treealig.tar.Z.
Update: 23-Nov-1990.
Version: Nov.
Size:
220 k
Compressed: TAR,.
Author:
Hein J.
Description:
Multiple sequence alignment and phylogeny
Literature:
Meth. Enzymol. 183 (1990), 626-644
Source Code:
C
SW Requirements:
-
HW Requirements:
-
File: sunuud.c.
Update: 19-Sep-1991.
Version: -.
Size:
20 k
Compressed: -.
Author:
Dumas M.
Description:
C source code for UUD uudecoder
Literature:
-
Source Code:
C
SW Requirements:
SUN C compiler
HW Requirements:
-
File: uud.c.
Update: 2-Apr-1991.
Version: -.
Size:
20 k
Compressed: -.
Author:
Dumas M.
Description:
C source code for UUD uudecoder
Literature:
-
Source Code:
C
SW Requirements:
ANSI C compiler
HW Requirements:
-
File: uue.c.
Update: 20-Jul-1990.
Version: -.
Size:
6 k
Compressed: -.
Author:
Dumas M.
Description:
C source code for UUE uuencoder
Literature:
-
Source Code:
C
SW Requirements:
-
HW Requirements:
-