FUCHS@embl.bitnet ("Rainer Fuchs ", EMBL) (01/03/90)
Here is the most recent directory listing of molecular biological programs
available from the EMBL File Server. We provide software for MS-DOS, VAX/VMS
and Apple Macintosh.
For introductory help send a mail message to NETSERV@EMBL containing the
lines
HELP
HELP SOFTWARE
Inquiries and submissions please direct to SOFTWARE@EMBL.
Directory of MS DOS Molecular Biology Software on EMBL File Server
------------------------------------------------------------------
To receive files from this directory use the command:
GET DOS_SOFTWARE:filename.ext
(a) Molecular Biology Software
filename ALX3$.UUE
version 1.0
size 140 k
compressed PAK
ASCII conversion UUE
author Gotoh O.
description Alignment of three protein or DNA sequences
literatur J. Theor. Biol. 121 (1986), 327-337
source code -
sw requirements -
hw requirements -
filename CMOLECUL.UUE
version May 87
size 70 k
compressed PAK
ASCII conversion UUE
author Thompson J. R. (Cedergren R.)
description graphics output of PCFOLD result files
literatur Nucl. Acids Res. 10 (1982), 8351-8356
source code available as MOLECSRC.UUE
sw requirements -
hw requirements CGA card
filename EMOLECUL.UUE
version May 87
size 70 k
compressed PAK
ASCII conversion UUE
author Thompson J. R. (Cedergren R.)
description graphics output of PCFOLD result files
literatur Nucl. Acids Res. 10 (1982), 8351-8356
source code available as MOLECSRC.UUE
sw requirements -
hw requirements EGA card
filename HMOLECUL.UUE
version May 87
size 70 k
compressed PAK
ASCII conversion UUE
author Thompson J. R. (Cedergren R.)
description graphics output of PCFOLD result files
literatur Nucl. Acids Res. 10 (1982), 8351-8356
source code available as MOLECSRC.UUE
sw requirements -
hw requirements Hercules card
filename MOLECSRC.UUE
version May 87
size 70 k
compressed PAK
ASCII conversion UUE
author Thompson J. R. (Cedergren R.)
description Source code for MOLECULE
literatur Nucl. Acids Res. 10 (1982), 8351-8356
source code Pascal
sw requirements Turbo Pascal
hw requirements -
filename EZ-FIT$.UUE
version 1.1
size 170 k
compressed PAK
ASCII conversion UUE
author Perella F. W.
description Calculation of enzyme and receptor kinetics
literatur Anal. Biochem. 174 (1989), 437-447
source code -
sw requirements -
hw requirements CGA card
filename GEL$.UUE
version 17.2.89
size 50 k
compressed PAK
ASCII conversion UUE
author Thompson J. R.
description Calculation of DNA restriction fragment sizes
literatur Anal. Biochem. 115 (81), 113-122
source code Pascal
sw requirements (Turbo Pascal for recompiling)
hw requirements -
filename HYDRASC$.UUE
version 1
size 30 k
compressed PAK
ASCII conversion UUE
author Penttila T. J.
description Contour map for two polypeptide sequences.
Regions with similar hydropathic properties and second.
structure properties are plotted.
literatur CABIOS, in prep.
source code -
sw requirements MATLAB-PC
hw requirements Math. co-processor, >2M RAM
filename MOTIF$.UUE
version - (bug fix with plain ASCII sequences)
size 45 k
compressed PAK
ASCII conversion UUE
author Giles I.
description Motif searching program
literatur CABIOS 5 (1989), 227-232
source code C
sw requirements (Turbo C for recompiling)
hw requirements -
filename OLIGO.UUE
version 1.0
size 105 k
compressed PAK
ASCII conversion UUE
author Beadles K.
description Oligo-directed single amino acid substitution
literatur -
source code -
sw requirements -
hw requirements -
filename PATTERN$.UUE
version -
size 55 k
compressed PAK
ASCII conversion UUE
author Giles I.
description Pattern searching program
literatur CABIOS 5 (1989), 227-232
source code C
sw requirements (Turbo C for recompiling)
hw requirements -
filename PCFOLD$.UUE
version 4.0
size 160 k
compressed PAK
ASCII conversion UUE
author Zuker M.
description RNA folding
literatur Meth. Enzymology 180 (1989), 262-288
source code Fortran, Asm
sw requirements (Compiler for recompiling)
hw requirements -
filename PLASMID.UUE
version 1.1
size 75 k
compressed PAK
ASCII conversion UUE
author Lipsick J.
description Plasmid drawing program (CGA card req.)
literatur -
source code Basic
sw requirements (Quickbasic for recompiling)
hw requirements CGA card
filename SDSE.UAA
version 2.0
size 185 k
compressed PAK
ASCII conversion UUE (split)
author Oliver J. L.
description Simulation of DNA sequence evolution (Part 1 of 2)
literatur CABIOS 5 (1989), 47-50
source code -
sw requirements -
hw requirements -
filename SDSE.UAB
version 2.0
size 50 k
compressed PAK
ASCII conversion UUE (split)
author Oliver J. L.
description Simulation of DNA sequence evolution (Part 2 of 2)
literatur CABIOS 5 (1989), 47-50
source code -
sw requirements -
hw requirements -
filename SEQAIDFD.UAA
version 3.5
size 185 k
compressed PAK
ASCII conversion UUE (split)
author Roufa D.
description DNA and protein sequence analysis package (Part 1 of 2)
literatur -
source code -
sw requirements -
hw requirements -
filename SEQAIDFD.UAB
version 3.5
size 185 k
compressed PAK
ASCII conversion UUE (split)
author Roufa D.
description DNA and protein sequence analysis package (Part 2 of 2)
literatur -
source code -
sw requirements -
hw requirements -
filename SIGSEQ$.UUE
version 1.0
size 60 k
compressed PAK
ASCII conversion UUE
author Popowicz A.M.
description Prediction of signal sequence cleavage site
literatur CABIOS 4 (1988), 405-406
source code C
sw requirements (Compiler for recompiling)
hw requirements -
filename TDALIGN$.UUE
version 1.61
size 120 k
compressed PAK
ASCII conversion UUE
author Davison D. (Thompson K.)
description Sequence alignment
literatur -
source code -
sw requirements -
hw requirements -
(b) Archiving/Decoding Software
filename UUEMBL.UUE
version -
size 35 k
compressed PAK
ASCII conversion UUE
author Fuchs R. (Dumas M.)
description UUEncoded form of UUD uudecoder and UUE uuencoder
literatur -
source code C
sw requirements -
hw requirements -
filename UUD.C
version -
size 20 k
compressed no
ASCII conversion no
author Dumas M.
description Source code for recommended uudecoder
literatur -
source code C
sw requirements Turbo C
hw requirements -
filename UUDECODE.PAS
version modified 4-Dec-1989
size 6 k
compressed no
ASCII conversion no
author -
description Source code for bootstrap uudecoder
literatur -
source code Pascal
sw requirements Turbo Pascal
hw requirements -
filename UUD19.BAS
version -
size 5 k
compressed no
ASCII conversion no
author -
description Source code for bootstrap uudecoder
literatur -
source code Basic
sw requirements GWBasic
hw requirements -
Files with the extension ".uue", ".uaa" etc. must be decoded with UUD.
See HELP DOS_SOFTWARE for details.
To get a listing of *all* software files available from the EMBL File Server
send the command GET ALL_SOFTWARE to NETSERV@EMBL.
Directory of Apple Macintosh Molecular Biology Software on EMBL File Server
---------------------------------------------------------------------------
To receive files from this directory use the command:
GET MAC_SOFTWARE:filename.ext
filename BUFSTACK.HQX
version 1.1
size 80 k
compressed StuffIt
ASCII conversion StuffIt
author Beynon R. J.
description Calculation of thermodynamically-corrected buffer recipes
literatur CABIOS 4 (1988), 487-490
source code -
sw requirements HyperCard
hw requirements -
filename DNAID.HQX
version 1.1
size 230 k
compressed StuffIt
ASCII conversion StuffIt
author Dardel F.
description DNA sequence editor with grep-like search routine
literatur CABIOS 4 (1988), 483-486
source code -
sw requirements -
hw requirements -
filename DOTTYPLOT.HQX
version 1.0c
size 210 k
compressed StuffIt
ASCII conversion StuffIt
author Gilbert D.
description Dot-matrix comparison of DNA sequences
literatur -
source code Pascal source for sequence loading subroutine
sw requirements -
hw requirements -
filename ENZYMEKIN.HQX
version 1.0
size 105 k
compressed StuffIt
ASCII conversion StuffIt
author Gilbert D.
description Calculation of enzyme kinetics
literatur -
source code HyperTalk
sw requirements HyperCard
hw requirements -
filename GELFRAG.HQX
version 1.4
size 145 k
compressed StuffIt
ASCII conversion StuffIt
author Gilbert D.
description Calculation of DNA restriction fragment sizes
literatur -
source code HyperTalk
sw requirements HyperCard
hw requirements -
filename MACDNA.HQX
version 2/88
size 65 k
compressed StuffIt
ASCII conversion StuffIt
author Schleif R.
description DNA sequence analysis, ported from IBM-PC
literatur -
source code -
sw requirements -
filename MATMETH.HQX
version 3.1
size 225 k
compressed StuffIt
ASCII conversion StuffIt
author Brown J.
description Molecular biological protocols
literatur -
source code HyperTalk
sw requirements HyperCard
hw requirements -
filename RRNA1.HQX
version 0.3
size 165 k
compressed StuffIt
ASCII conversion StuffIt
author Brown J.
description Phylogeny of 16/18S rRNA (part 1 of 2)
literatur -
source code HyperTalk
sw requirements HyperCard
hw requirements -
filename RRNA2.HQX
version 0.3
size 120 k
compressed StuffIt
ASCII conversion StuffIt
author Brown J.
description Phylogeny of 16/18S rRNA (part 2 of 2)
literatur -
source code HyperTalk
sw requirements HyperCard
hw requirements -
filename THREE.HQX
version -
size 80 k
compressed StuffIt
ASCII conversion StuffIt
author Markiewicz P. (Johnson M.)
description Alignment of three protein sequences
literatur -
source code -
sw requirements -
hw requirements -
Files with the extension ".hqx" have to be decoded by (Un)StuffIt.
To get a listing of *all* software files available from the EMBL File Server
send the command GET ALL_SOFTWARE to NETSERV@EMBL.
Directory of VAX Molecular Biology Software on EMBL File Server
---------------------------------------------------------------
To receive files from this directory use the command:
GET VAX_SOFTWARE:filename.ext
(a) Molecular Biology Software
filename BUGFIX_6_1.GCG
version -
size 9 k
compressed -
ASCII conversion -
author -
description Fixes for several bugs in GCG package v6.1
literatur -
source code -
sw requirements GCG package,Fortran compiler, C compiler
hw requirements -
filename CLUSTAL.UUE
version -
size 90 k
compressed ZOO
ASCII conversion UUE
author Higgins D.
description Multiple sequence alignment
literatur Gene 73 (1988), 237
source code Fortran
sw requirements VAX Fortran for recompiling
hw requirements -
filename GCGEMBL.UAA
version -
size 180 k
compressed ZOO
ASCII conversion UUE (split)
author Rice P.
description GCG extensions developed at EMBL (part 1 of 2)
literatur -
source code Fortran
sw requirements GCG package v5 or v6
hw requirements -
filename GCGEMBL.UAB
version -
size 165 k
compressed ZOO
ASCII conversion UUE (split)
author Rice P.
description GCG extensions developed at EMBL (part 2 of 2)
literatur -
source code Fortran
sw requirements GCG package v5 or v6
hw requirements -
filename MOTIF.UUE
version -
size 90 k
compressed ZOO
ASCII conversion UUE
author Giles I.
description Motif searching program
literatur CABIOS 5 (1989), 227-232
source code C
sw requirements VAX C for recompiling
hw requirements -
filename PATTERN.UUE
version -
size 100 k
compressed ZOO
ASCII conversion UUE
author Giles I.
description Pattern searching program
literatur CABIOS 5 (1989), 227-232
source code C
sw requirements VAX C for recompiling
hw requirements -
filename SHELLS.GCG
version -
size 90 k
compressed -
ASCII conversion -
author Clark S.
description DCL shells for many GCG programs
literatur -
source code DCL, Fortran
sw requirements VAX Fortran
hw requirements -
(b) Decoding Software
filename UUD.C
version -
size 20 k
compressed no
ASCII conversion no
author Dumas M.
description C source code for UUD uudecoder
literatur -
source code C
sw requirements VAX C
hw requirements -
filename ZOO.UUE
version -
size 60 k
compressed no
ASCII conversion UUE
author Dhesi R.
description Archiving program
literatur -
source code -
sw requirements -
hw requirements -
(c) Other software
filename CD_ACCESS.TXT
version -
size 145 k
compressed -
ASCII conversion -
author Stockwell P.A.
description Driver software for ISO-formatted CD-ROMs
literatur -
source code Pascal
sw requirements VAX Pascal
hw requirements CD-ROM drive
Files with the extension ".uue", ".uaa" et. must be decoded by UUD. The
resulting ZOO-archives have to be extracted by ZOO. See HELP VAX_SOFTWARE for
details.
To get a listing of *all* software files available from the EMBL File Server
send the command GET ALL_SOFTWARE to NETSERV@EMBL.
General software
----------------
To receive any of these files use the command:
GET SOFTWARE:filename.ext
Software submission form v. ESW2.89 - Filename: SUBMISSION.SW
To facilitate software submission to the EMBL File Server.
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