From NETSERV@EMBL-Heidelberg.DE Fri Sep 6 13:58:30 1991 Received: from sirius.EMBL-Heidelberg.DE by sunflower.bio.indiana.edu (4.1/9.5jsm) id AB06317; Fri, 6 Sep 91 13:57:42 EST Date: Fri, 6 Sep 1991 14:50 +0100 From: NETSERV@EMBL-Heidelberg.DE Subject: Reply to: HELP UNIX_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 UNIX_SOFTWARE [DIR UNIX_SOFTWARE] UNIX Molecular Biology Software on EMBL File Server -------------------------------------------------- Molecular biological software for the UNIX operating system 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 --------------- UNIX 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 UNIX_SOFTWARE:UUD.C and compile it: % cc -o uud uud.c SUN users should get the file SunUUD.C instead of UUD.C, because the SUN C compiler does not support the ANSI C standard (SUN users may alternatively use the GNU C compiler to compile uud.c). The programs that are used for data compression are the standard UNIX tar and compress programs. How to access files ------------------- All software for UNIX on the EMBL File Server is in a directory called UNIX_SOFTWARE, and a directory listing can be acquired with the file server command: DIR UNIX_SOFTWARE To get any specific file use the command: GET UNIX_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. In most cases, the file name will end with .tar.Z Now use the UNIX uncompress program to expand these files: % uncompress filename.tar.Z which will result in a file named filename.tar in your current directory. Finally, use tar to extract all files from these archives: % tar -xvf filename.tar 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 UNIX program SIGSEQ use the command: GET UNIX_SOFTWARE:SIGSEQ.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 UNIX Molecular Biology Software on EMBL File Server --------------------------------------------------------------- To receive files from this directory use the command: GET UNIX_SOFTWARE:filename.ext (a) Molecular Biology Software filename BLAST.UAA update 26-Oct-1990 version - size 200 k compressed TAR, COMPRESS ASCII conversion UUE (split; will be sent in 3 parts: .UAA to .UAC) 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 and LIBNCBI are required! hw requirements - filename CLUSTALV.UAA update 8-Aug-1991 version 5 size 120 k compressed TAR, COMPRESS 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 ANSI C compiler or GNU 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 DFA.UAA update 12-Nov-1990 version - size 125 k compressed TAR, COMPRESS ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB) 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 - filename FILTER.UAA update 8-Aug-1991 version - size 240 k compressed TRAR,COMPRESS 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 sw requirements - hw requirements SUN 2,3 or 4 filename GDE1_0.UAA update 1-Jul-1991 version 1.0 size 380 k compressed TAR, COMPRESS ASCII conversion UUE (split; will be sent in 5 parts: .UAA to .UAE) 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 filename GDE_DOC.UAA update 1-Jul-1991 version 1.0 size 550 k compressed TAR, COMPRESS ASCII conversion UUE (split; will be sent in 7 parts: .UAA to .UAG) author Harvard Genome Lab description Expandable set of programs for multiple sequence alignment and analysis (documentation - Postscript) literature - source code - sw requirements - hw requirements - filename GDE_SRC.UAA update 1-Jul-1991 version 1.0 size 400 k compressed TAR, COMPRESS ASCII conversion UUE (split; will be sent in 5 parts: .UAA to .UAE) 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 filename GM.UAA update 23-Jul-1990 version - size 360 k compressed TAR, COMPRESS ASCII conversion UUE (split; will be sent in 4 parts: .UAA to .UAD) 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 - filename HOMOCHART.UUE update 3-Apr-1991 version - size 20 k compressed TAR, COMPRESS ASCII conversion UUE author Smith R. description Plotting multiple sequence alignments with boxes around identical residues literature - source code C sw requirements - hw requirements - filename ISSC.UAA update 26-Jul-1991 version - size 580 k compressed TAR,COMPRESS 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 - hw requirements SUN 2,3 or 4 filename LIBNCBI.UAA update 26-Oct-1990 version - size 115 k compressed TAR, COMPRESS ASCII conversion UUE (split; will be sent in 2 parts: .UAA and .UAB) 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 - filename MASE.UAA update 30-Jul-1990 version - size 930 k compressed TAR, COMPRESS ASCII conversion UUE (split; will be sent in 11 parts: .UAA to .UAK) author Faulkner D. V. description Multiple sequence editor literature TIBS 13 (1989), 321-322 source code C sw requirements - hw requirements - filename MFASTA.UUE update 31-Jul-1990 version 1.2 size 21 k compressed - ASCII conversion UUE author deBoer T. description Script for using EMBL/GenBank Mail-FASTA servers literature - source code C sw requirements - hw requirements - filename NSEQTOOL.UAA update 31-Jul-1991 version - size 340 k compressed TAR, COMPRESS ASCII conversion UUE (split; will be sent in 4 parts: .UAA to .UAD) author Schnobel R. description Integrated displays 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 filename OVERSEER.UUE update 23-May-1991 version 1.0 size 65 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 - hw requirements - filename PIMA.UAA update 1-Jul-1991 version 1.0 size 680 k compressed TAR, COMPRESS ASCII conversion UUE (split; will be sent in 8 parts: .UAA to .UAH) 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 - filename PLSEARCH.UAA update 21-Aug-1990 version 4.0 size 2550 k compressed TAR, COMPRESS ASCII conversion UUE (split; will be sent in 30 parts: .UAA to .UBD) author Smith, R.F. and Smith T.F. description Pattern detection in proteins literature - source code C sw requirements - hw requirements - filename PROSEARCH.UAA update 24-Jan-1991 version 1.2 size 85 k compressed TAR, COMPRESS 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 SEQF.UAA update 12-Feb-1991 version - size 140 k compressed TAR, COMPRESS ASCII conversion UUE (split; will be sent in 3 parts: .UAA to .UAC) author Davison D. and Kanehisa M. description Package of programs for searching genetic sequence libraries. literature - source code Fortran sw requirements - hw requirements - filename SIGSEQ.UUE update 19-Jul-1990 version - size 20 k compressed TAR, COMPRESS ASCII conversion UUE author Popowicz A.M. description Prediction of signal sequence cleavage site literature CABIOS 4 (1988), 405-406 source code C sw requirements - hw requirements - filename SIM.UUE update 7-Nov-1990 version - size 30 k compressed TAR, COMPRESS 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 110 k compressed TAR, COMPRESS 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 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 TAR, COMPRESS 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 - hw requirements - (b) Decoding Software 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 - hw requirements - filename UUE.C update 20-Jul-1990 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 - hw requirements - 8-Aug-1991