From NETSERV@EMBL-Heidelberg.DE Fri Sep 6 13:57:37 1991 Received: from sirius.EMBL-Heidelberg.DE by sunflower.bio.indiana.edu (4.1/9.5jsm) id AB06317; Fri, 6 Sep 91 13:55:58 EST Date: Fri, 6 Sep 1991 14:50 +0100 From: NETSERV@EMBL-Heidelberg.DE Subject: Reply to: HELP VAX_SOFTWARE To: gilbertd@sunflower.bio.indiana.edu Errors-To: PostMaster@EMBL-Heidelberg.DE Message-Id: X-Organization: European Molecular Biology Laboratory, Heidelberg. X-Envelope-To: gilbertd@sunflower.bio.indiana.edu X-Vms-To: in%"gilbertd@sunflower.bio.indiana.edu" Status: R HELP VAX_SOFTWARE VAX Molecular Biology Software on EMBL File Server -------------------------------------------------- Molecular biological software for the DEC VAX running VMS is available from the EMBL File Server. Though all programs are tested we can make no warranty on the functionality of these programs nor shall be liable for any damage resulting from their usage. Most programs on the File Server are freeware, but that does not imply that there are no rights reserved by the authors. Some programs are shareware. You may freely copy and distribute these programs, but if you like to use them after a trial period you are asked to send the author a small fee. Please see the accompanying documentation files or manuals for details of copyright status. To get any file from the EMBL File Server use normal E-mail addressed to NETSERV@EMBL-Heidelberg.DE. The body of the mail message should contain one server command per line. Getting started --------------- VAX software on the EMBL File Server is distributed in a form that is first compressed and then converted from binary to printable ASCII ("uuencoded"). The standard extension for uuencoded files is ".uue". You will first need to install the decoding program UUD on your machine. Get the C source code from the EMBL File Server using the command: GET VAX_SOFTWARE:UUD.C and compile and link it: $ cc uud $ link uud,sys$library:vaxcrtl/lib The program that is applied for compressing VMS files is called "ZOO". It is available in uuencoded form from the file server. GET VAX_SOFTWARE:ZOO.UAA Follow the procedure given below to decode it to ZOO.EXE. To be able to run these program insert the following lines in your login.com procedure: $ UUD :== $ your_directory:UUD $ ZOO :== $ your_directory:ZOO your_directory must be replaced by the name of the directory where these programs are actually located, including the disk name. For example, if the disk name is $1, and the directory name is [myfiles], then you should use $ UUD :== $ $1:[myfiles]UUD Note: if you are using a version of VMS less than 5.2 and encounter problems running ZOO, you should instead download VAX_SOFTWARE:OLDZOO.UUE from the server, and use this older version of ZOO. How to access files ------------------- All software for VAX VMS on the EMBL File Server is in a directory called VAX_SOFTWARE, and a directory listing can be acquired with the file server command: DIR VAX_SOFTWARE To get any specific file use the command: GET VAX_SOFTWARE:filename.ext For decoding a uuencoded file run UUD and specify the source file name: $ UUD filename.UUE Files larger than 100k are split into parts. The first part is designated "filename.UAA", the second part "filename.UAB" and so forth. If you send a request for "filename.UAA", you will automatically receive all parts of a package. The Subject line will tell you the part number of each part and how many parts were sent in total. To decode split files follow this procedure: Extract all files from your mail reader to your disk. Call part 1 of a package "filename.UAA", part 2 "filename.UAB", and so on. Make sure that all belonging parts are in one directory and type: $ UUD filename.UAA The name of the resulting file after UUDecoding is stored within the ".uaa" or ".uue" file; it will be placed in your current directory. It will in most cases have the extension ".ZOO". These ZOO-archives have to be extracted by ZOO to obtain the executable programs and documentation. Use the command: $ ZOO E filename This will extract all files contained in the archive into your default directory. Record of requests ------------------ To facilitate communication between users of provided software and to give software authors some information on who has obtained copies of their programs, the File Server keeps a log of requests for each program by storing the sender's E-mail address in a file named "filename.LOG". For example, to get the log for the VAX/VMS program CLUSTALV use the command: GET VAX_SOFTWARE:CLUSTALV.LOG Problems -------- If you have any problems or questions contact: EMBL Data Library Meyerhofstr. 1 D-6900 Heidelberg, FRG tel.: +49-6221-387258 E-mail: SOFTWARE@EMBL-Heidelberg.DE 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 ALIGN_X.UAA update 8-Aug-1991 version - size 540 k compressed ZOO ASCII conversion UUE (split; will be sent in 6 parts: .UAA to .UAF) 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 DEC-Windows (UIS version is ISSC.UAA) hw requirements - filename AMPHI.UUE update 12-Apr-1990 version - size 30 k compressed ZOO ASCII conversion UUE author Jaehnig F. description Prediction of membran protein structure literature Trends in Biochemistry 3 (1990) source code Fortran sw requirements GCG v6 for plotting (works without GCG) hw requirements - filename BOXSHADE.UAA update 1-Aug-1991 version 2.3a size 140 k compressed ZOO ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB) author Hoffmann K. description Plots multiple alignments, marking identical or similar residues literature - source code Pascal sw requirements - hw requirements - filename BUGFIX_6_1.GCG update 18-Dec-1989 version - size 9 k compressed - ASCII conversion - author - description Fixes for several bugs in GCG package v6.1 literature - source code - sw requirements GCG package,Fortran compiler, C compiler hw requirements - filename CKIT.UAA update 2-Aug-1990 version 2.1 size 245 k compressed ZOO ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB) author Gilbert W.A. description C toolbox for writing sequence analysis programs literature - source code - sw requirements VAX C compiler hw requirements - filename CLUSTALV.UAA update 8-Aug-1991 version 5 size 120 k compressed ZOO ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB) author Higgins D., Fuchs R. and Bleasby D. description Multiple sequence alignment literature CABIOS, in press source code C sw requirements C compiler hw requirements - filename CREGEX.C update 12-Jan-1991 version 1.1 size 10 k compressed - ASCII conversion - author Leunissen J. description Reformating of Prosite for use with Kolakowski's PROSEARCH literature - source code C sw requirements (used by PROSEARCH [PROSEARCH.UAA]) hw requirements - filename DBCONV.HQX update 14-Jun-1991 version 1.0 size 20 k compressed ZOO ASCII conversion UUE author Valverde J.R. description Transformation of line-oriented databases into tab- delimited format literature - source code C sw requirements - hw requirements - filename FASTEMBL.COM update 5-Dec-1990 version 1.1 size 15k compressed ZOO ASCII conversion UUE author Sonnhammer E. L. (Clark S.) description DCL shell for facilitating EMBL Mail-FASTA access literature - source code DCL sw requirements - hw requirements - filename FILTER.UAA update 8-Aug-1991 version - size 240 k compressed ZOO ASCII conversion UUE (split; will be sent in 3 parts: .UAA to .UAC) 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, Fortran sw requirements UIS hw requirements - filename GCGDBASE.UAA update 23-Mar-1990 version - size 120 k compressed ZOO ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB) author Rice P. description GCG extensions developed at EMBL for using new EMBL distribution format literature - source code Fortran sw requirements GCG package v6 hw requirements - filename GCGEMBL.UAA update 30-Oct-1989 version - size 180 k compressed ZOO ASCII conversion UUE (split; will be sent in 4 parts: .UAA to .UAD) author Rice P. description GCG extensions developed at EMBL literature - source code Fortran sw requirements GCG package v5 or v6 hw requirements - filename GCGQUICK.UAA update 25-Apr-1990 version - size 150 k compressed ZOO ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB) author Rice P. description GCG extensions developed at EMBL for speeding up QuickSearch literature - source code Fortran sw requirements GCG package v6 hw requirements - filename GCGSHELLS1.TXT update 7-May-1990 version May 1990 size 90 k compressed - ASCII conversion - author Clark S. description DCL shells for many GCG programs literature - source code DCL, Fortran sw requirements VAX Fortran hw requirements - filename GCGSHELLS2.TXT update 13-Mar-1990 version - size 90 k compressed - ASCII conversion - author Clark S. description DCL shells to facilitate GenBank on-line service access literature - source code DCL, Fortran sw requirements VAX Fortran hw requirements - filename ISSC.UAA update 26-Jul-1991 version - size 580 k compressed ZOO ASCII conversion UUE (split; will be sent in 7 parts: .UAA to .UAG) 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 UIS (DEC-Windows version is ALIGN_X.UAA) hw requirements - filename MALFORM.UUE update 24-Jul-1991 version 1.0 size 25 k compressed ZOO ASCII conversion UUE author Clark S. description Conversion of MALIGNED output to PostScript literature - source code - sw requirements MALIGNED (available as MALIGNED.UAA) hw requirements - filename MALIGNED.UAA update 27-Jun-1991 version 1 size 120 k compressed ZOO ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB) author Clark S. description Multiple sequence editor literature - source code - sw requirements - hw requirements - filename MOTIF.UUE update 9-Nov-1989 version - size 90 k compressed ZOO ASCII conversion UUE author Giles I. description Motif searching program literature CABIOS 5 (1989), 227-232 source code C sw requirements VAX C for recompiling hw requirements - filename MSE.UUE update 2-Aug-1990 version 2.0 size 90 k compressed ZOO ASCII conversion UUE author Gilbert W.A. description Multiple sequence editor literature - source code - sw requirements - hw requirements - filename NOCUT.COM update 21-Aug-1990 version 21-Aug-1990 size 12 k compressed - ASCII conversion - author Easton T. description Production of restriction enzyme database file of non-cutters taken from MAP output for use with MAP/SIL. literature - source code DCL sw requirements GCG hw requirements - filename OVERSEER.UUE update 28-Aug-1991 version _ size 75 k compressed ZOO ASCII conversion UUE author Sibbald P. description A package for searching nucleic acid sequence data bases literature CABIOS, submitted source code Pascal sw requirements VAX Pascal for recompiling hw requirements - filename PATTERN.UAA update 9-Nov-1989 version - size 100 k compressed ZOO ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB) author Giles I. description Pattern searching program literature CABIOS 5 (1989), 227-232 source code C sw requirements VAX C for recompiling hw requirements - filename PROFILESCAN.BUGFIX update 7-Sep-1990 version - size 4 k compressed - ASCII conversion - author Gribskov M. description Bug fix for the GCG program PROFILESCAN literature - source code - sw requirements GCG package,Fortran compiler hw requirements - filename PROINDEX.UUE update 1-Jun-1990 version - size 45 k compressed - ASCII conversion - author Clark S. description Index file creation for ProSite pattern database literature - source code Fortran sw requirements VAX Fortran hw requirements - filename PROSEARCH.UAA update 24-Jan-1991 version 1.2 size 80 k compressed ZOO ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB) author Kolakowski L. F. description Pattern searching in proteins using Prosite (incl. CREGEX.C and TFD2PROSITE.C) literature - source code C sw requirements Awk hw requirements - filename PROSITEC.UUE update 7-Jun-1990 version 1.1 size 40 k compressed ZOO ASCII conversion UUE author Hofmann K. description Conversion of Prosite database to GCG Find format literature - source code Pascal sw requirements VAX Pascal for recompiling hw requirements - filename READSEQ.UUE update 28-Aug-1991 version October 1990 size 75 k compressed ZOO ASCII conversion UUE author Gilbert D. description Multiple sequence format conversion program literature - source code C, Pascal sw requirements VAX C for recompiling hw requirements - filename RST_OLAP.UUE update 5-Oct-1990 version 1.0 size 45 k compressed ZOO ASCII conversion UUE author Stockwell P. A. description Creates sorted list of restrictione enzymes giving adhesive ends from REBASE database file literature - source code Pascal sw requirements - hw requirements - filename SCRUTINE.UAA update 7-Jun-1991 version November 1990 size 720 k compressed ZOO ASCII conversion UUE (split; will be sent in 12 parts: .UAA to .UAL) author Sibbald P. description SCRUTINEER: a package for searching protein sequence databases literature CABIOS 6 (1990), 279-288 source code Pascal sw requirements VAX Pascal for recompiling hw requirements - filename SEQEDT.UUE update 2-Aug-1990 version 2.0 size 80 k compressed ZOO ASCII conversion UUE author Gilbert W.A. description Sequence editor, modelled on EDT literature - source code - sw requirements - hw requirements - filename SIM.UUE update 12-Feb-1991 version - size 30 k compressed ZOO ASCII conversion UUE author Huang G. and Miller W. description Local similarity searching literature CABIOS 6 (1990), 373 - 381. source code C sw requirements - hw requirements - filename SSCAN.UAA update 8-Jul-1991 version 2.1 size 130 k compressed ZOO ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB) 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 - filename STATSRCH.UAA update 18-May-1990 version - size 145 k compressed ZOO ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB) author Mott R. F. description Database searching taking into account the statistical significance of any similarities found literature CABIOS, 6 (1990), 293-295 source code Fortran sw requirements GCG package hw requirements - filename SUBFORM.UAA update 28-Aug-1991 version - size 145 k compressed ZOO ASCII conversion UUE (split; will be sent in 9 parts: .UAA to .UAI) author Spaulding M. and Kyne T. description Program which helps to prepare sequence data submissions literature - source code Pascal, Fortran sw requirements - hw requirements - filename TFD2PROSITE.C update 25-Feb-1991 version 1.1 size 10 k compressed - ASCII conversion - 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 - filename TREEALIG.UAA update 23-Nov-1990 version Nov 1990 size 300 k compressed ZOO ASCII conversion UUE (split; will be sent in 4 parts: .UAA to .UAD) author Hein J. description Multiple sequence alignment and phylogeny literature Meth. Enzymol. 183 (1990), 626-644 source code C sw requirements VAX C for recompiling hw requirements - (b) Decoding Software filename OLDZOO.UUE update 27-Jun-1990 version 1.6 (1-Aug-1987) size 55 k compressed no ASCII conversion UUE author Dhesi R. description Archiving program literature - source code - sw requirements - hw requirements - filename UUD.C update 2-Apr-1991 version - size 20 k compressed no ASCII conversion no author Dumas M. description C source code for UUD uudecoder literature - source code C sw requirements VAX C hw requirements - filename UUE.C update 25-Sep-1989 version - size 6 k compressed no ASCII conversion no author Dumas M. description C source code for UUE uuencoder literature - source code C sw requirements VAX C hw requirements - filename ZOO.UAA update 26-Jul-1991 version 2.1 size 200 k compressed no ASCII conversion UUE (split; will be sent in 3 parts: .UAA to .UAC) author Dhesi R. description Archiving program literature - source code - sw requirements - hw requirements - (c) Other software filename CDACCESS.UAA update Feb-1991 version 2.05 size 180 k compressed ZOO ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB) author Stockwell P.A. description Driver software for ISO-formatted CD-ROMs literature - source code Pascal sw requirements VAX Pascal hw requirements CD-ROM drive 28-Aug-1991