From NETSERV@EMBL-Heidelberg.DE Fri Sep 6 13:55:54 1991 Received: from sirius.EMBL-Heidelberg.DE by sunflower.bio.indiana.edu (4.1/9.5jsm) id AB06317; Fri, 6 Sep 91 13:53:49 EST Date: Fri, 6 Sep 1991 14:50 +0100 From: NETSERV@EMBL-Heidelberg.DE Subject: Reply to: HELP MAC_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 MAC_SOFTWARE [DIR MAC_SOFTWARE] Apple Macintosh Molecular Biology Software on EMBL File Server -------------------------------------------------------------- Molecular biological software for the Apple Macintosh 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 --------------- The Macintosh software on the EMBL File Server is distributed in a form that is first compressed and then converted from binary to printable ASCII. The program that is used to compress and encode Macintosh files is called Compactor (or Compact Pro). The result of the compression process is a self- extracting archive, i.e. you simply double-click on it and it will create all the files that comprise the downloaded software package. For mail transfer these binary archives are converted to ASCII (binhexed). The standard extension for these files is ".hqx". To properly decode them you will first need to get a copy of a program that reverts the binhexing procedure. A couple of programs is available for this purpose, such as BinHex4, StuffIt, Compact Pro, BinHqx, etc. Since no source code is available please ask your Macintosh user group or your local Mac guru for these programs. How to access files ------------------- All software for the Macintosh on the EMBL File Server is in a directory called MAC_SOFTWARE, and a directory listing can be acquired with the file server command: DIR MAC_SOFTWARE To get any specific file use the command: GET MAC_SOFTWARE:filename.ext Transfer this file to your Macintosh (e. g. using Kermit with file type set to ASCII). For decoding a binhexed file run BinHex, StuffIt, Compactor etc., and use the option "Decode BinHex-File". The resulting file is a self- extracting archive. Simply double-click on its icon to install the software. Very large files are split into parts. Use any word processor to remove the header lines and join the parts. Make sure to save the resulting file in text-only mode. Then use BinHex or a similar program for conversion. 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 Mac program MATMETH use the command: GET MAC_SOFTWARE:MATMETH.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 Apple Macintosh Molecular Biology Software on EMBL File Server --------------------------------------------------------------------------- To receive files from this directory use the command: GET MAC_SOFTWARE:filename.ext (a) Molecular Biology Software filename BUFSTACK.HQX update 17-Nov-1989 version 1.1 size 80 k compressed Compactor (self-extracting) ASCII conversion BinHex author Beynon R. J. description Calculation of thermodynamically-corrected buffer recipes literature CABIOS 4 (1988), 487-490 source code - sw requirements HyperCard hw requirements - filename CGR.HQX update 10-Aug-1990 version 1.0 size 40 k compressed Compactor (self-extracting) ASCII conversion BinHex author Lehvaslaiho H. description Chaos game representation of DNA sequences literature - source code HyperTalk sw requirements HyperCard hw requirements - filename CHEMINVENTORY.HQX update 19-Aug-1991 version 2.1 size 244 k compressed Compactor (self-extracting) ASCII conversion BinHex author Swartling D. description HyperCard stack to keep track of a large chemical inventory literature - source code HyperTalk sw requirements HyperCard 2.0 hw requirements - filename CLUSTALV.HQX update 8-Aug-1991 version 5 size 160 k compressed Compactor (self-extracting) ASCII conversion BinHex author Higgins D., Fuchs R. and Bleasby D. description Multiple sequence alignment literature CABIOS, in press source code C sw requirements - hw requirements 2 MB memory filename COVARIATION.HQX update 30-Jul-1991 version 2.3 size 115k compressed Compactor (self-extracting) ASCII conversion BinHex author Brown J. description Identification of compensating bas changes and covariations in aligned RNA sequences literature CABIOS 7 (1991), 391-393 source code HyperTalk sw requirements HyperCard 2.0 hw requirements - filename DBCONV.HQX update 14-Jun-1991 version 1.0 size 140 k compressed Compactor (self-extracting) ASCII conversion BinHex author Valverde J.R. description Transformation of line-oriented databases into tab- delimited format literature - source code C sw requirements - hw requirements - filename DNAID.HQX update 19-Oct-1989 version 1.1 size 230 k compressed Compactor (self-extracting) ASCII conversion BinHex author Dardel F. description DNA sequence editor with grep-like search routine literature CABIOS 4 (1988), 483-486 source code - sw requirements - hw requirements - filename DNATRANSLATOR.HQX update 23-May-1991 version 0.99.1 size 505 k compressed Compactor (self-extracting) ASCII conversion BinHex author Eernisse D. J. description HyperCard stack with utilities for phylogenetic analyses and sequence manipulations literature - source code HyperTalk sw requirements HyperCard 2.0 hw requirements - filename DOTTYPLOT.HQX update 20-Nov-1989 version 1.0c size 210 k compressed Compactor (self-extracting) ASCII conversion BinHex author Gilbert D. description Dot-matrix comparison of DNA sequences literature CABIOS 6 (1990), 117 source code Pascal source for sequence loading subroutine sw requirements - hw requirements - filename EMBL-SEARCH.HQX update 15-Apr-1991 version 1.0 size 140 k compressed Compactor (self-extracting) ASCII conversion BinHex author Fuchs R. description Entry retrieval from EMBL CD-ROM literature - source code Think C sw requirements - hw requirements EMBL CD-ROM filename ENDOCYTOSIS.HQX update 8-Nov-1990 version 0.1 size 150 k compressed Compactor (self-extracting) ASCII conversion BinHex author Williams R.E. description Calculation of parameters of endocytosis reaction literature - source code - sw requirements - hw requirements - filename ENZYMEKIN.HQX update 22-Sep-1989 version 1.0 size 105 k compressed Compactor (self-extracting) ASCII conversion BinHex author Gilbert D. description Calculation of enzyme kinetics literature CABIOS 6 (1990), 113-116 source code HyperTalk sw requirements HyperCard hw requirements - filename GELFRAG.HQX update 22-Sep-1989 version 1.4 size 145 k compressed Compactor (self-extracting) ASCII conversion BinHex author Gilbert D. description Calculation of DNA restriction fragment sizes literature CABIOS 6 (1990), 113-116 source code HyperTalk sw requirements HyperCard hw requirements - filename LOOPVIEWER.HQX update 6-Nov-1990 version 1.0 size 150 k compressed Compactor (self-extracting) ASCII conversion BinHex author Gilbert D. description Graphical representation of RNA folding literature - source code - sw requirements (MulFold is optional) hw requirements - filename MACCLADE.HQX update 20-Mar-1990 version 2.1 size 140 k compressed Compactor (self-extracting) ASCII conversion BinHex author Maddison W and Maddison D description Phylogeny program literature - source code - sw requirements - filename MACDNA.HQX update 24-Nov-1989 version 2/88 size 65 k compressed Compactor (self-extracting) ASCII conversion BinHex author Schleif R. description DNA sequence analysis, ported from IBM-PC literature - source code - sw requirements - filename MACLIGAND.HQX update 6-Nov-1990 version 1.02 size 115 k compressed Compactor (self-extracting) ASCII conversion BinHex author Williams R.E. description Calculation of parameters of ligand binding literature - source code - sw requirements - hw requirements - filename MACMOLECULE.HQX update 17-Jun-1991 version 1.5 size 400 k compressed Compactor (self-extracting) ASCII conversion BinHex author Myers E., Blanco C., Hallick R.B. and Jahnke J. description 3D models of biomolecules literature - source code - sw requirements - hw requirements - filename MACPATTERN.HQX update 5-Aug-1991 version 1.4 size 220 k compressed Compactor (self-extracting) ASCII conversion BinHex author Fuchs R. description Pattern searching in conjunction with Prosite database literature CABIOS 7 (1991), 105-106 source code - sw requirements (Prosite pattern database) hw requirements - filename MACPLASMAP.HQX update 28-Mar-1990 version 1.82 size 270 k compressed Compactor (self-extracting) ASCII conversion BinHex author Liu J. description Plasmid drawing program. literature - source code - sw requirements - filename MACTARGSEARCH.HQX update 29-Apr-1991 version 2.0 size 110 k compressed Compactor (self-extracting) ASCII conversion BinHex author Goodrich J.A., McClure W.R., and Schwartz M.L. description DNA profile searching literature Nucleic Acids Res. 18 (1990), 4993-5000 source code Basic sw requirements - hw requirements - filename MATMETH.HQX update 4-Mar-1991 version 5.0 size 150k compressed Compactor (self-extracting) ASCII conversion BinHex author Brown J. description Molecular biological protocols literature CABIOS 7 (1991), 397 source code HyperTalk sw requirements HyperCard 2.0 hw requirements - filename MINIMM.HQX update 16-Jan-1990 version 4.0 size 210 k compressed Compactor (self-extracting) ASCII conversion BinHex author Brown J. description Molecular biological protocols (more HyperCard-like) literature - source code HyperTalk sw requirements HyperCard hw requirements - filename MULFOLD.HQX update 6-Nov-1990 version 2.0 size 282 k compressed Compactor (self-extracting) ASCII conversion BinHex author Zuker M. description Calculation of RNA folding literature Science 244 (1989), 48-52 source code - sw requirements - hw requirements Math. co-processor filename MULTIDNA.HQX update 21-Jun-1991 version 1.0 size 25 k compressed Compactor (self-extracting) ASCII conversion BinHex author Gonzales R. description Editing of several DNA sequences simultaneously literature - source code - sw requirements HyperCard 2.0 hw requirements - filename READSEQ.HQX update 28-Aug-1991 version October 1990 size 70 k compressed Compactor (self-extracting) ASCII conversion BinHex author Gilbert D. description Pascal and C routines for handling different sequence file formats (EMBL,IG,Strider etc.) literature - source code Pascal, C sw requirements Pascal or C compiler hw requirements - filename REFSTACK.HQX update 16-Jan-1990 version 2.0 size 145 k compressed Compactor (self-extracting) ASCII conversion BinHex author Brown J. description Management of literature references literature - source code HyperTalk sw requirements HyperCard hw requirements - filename RIMANAGER.HQX update 6-Dec-1990 version 1.67 size 420 k compressed Compactor (self-extracting) ASCII conversion BinHex author Manly K. description Analysis of genetic mapping experiments with recombinant mouse strains. literature - source code - sw requirements - hw requirements - filename RRNA1.HQX update 30-Oct-1989 version 0.3 size 165 k compressed Compactor (self-extracting) ASCII conversion BinHex author Brown J. description Phylogeny of 16/18S rRNA (part 1 of 2) literature - source code HyperTalk sw requirements HyperCard hw requirements - filename RRNA2.HQX update 30-Oct-1989 version 0.3 size 120 k compressed Compactor (self-extracting) ASCII conversion BinHex author Brown J. description Phylogeny of 16/18S rRNA (part 2 of 2) literature - source code HyperTalk sw requirements HyperCard hw requirements - filename SEQLOGO.HQX update 4-Feb-1991 version ? size 500 k compressed Compactor (self-extracting) ASCII conversion BinHex author Schneider T. description Displaying consensus sequences by means of 'logos' literature Nucleic Acids Res. 18 (1990), 6097-6100 source code Pascal sw requirements - hw requirements - filename SEQSPEAK.HQX update 22-May-1991 version 1.0 size 220 k compressed Compactor (self-extracting) ASCII conversion BinHex author Conover K. description Sequence data entry with acoustic feedback literature - source code - sw requirements HyperCard 2.0 hw requirements - filename SPEAKQUENCER.HQX update 6-Nov-1990 version 1.1.1 size 100 k compressed Compactor (self-extracting) ASCII conversion BinHex author Fritze C. description Sequence data entry with acoustic feedback literature - source code - 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 THREE.HQX update 29-Sep-1989 version - size 80 k compressed Compactor (self-extracting) ASCII conversion BinHex author Markiewicz P. (Johnson M.) description Alignment of three protein sequences literature - source code - sw requirements - hw requirements - filename TREEDRAW.HQX update 26-Jun-1990 version - size 180 k compressed Compactor (self-extracting) ASCII conversion BinHex author Gilbert D. description Drawing of phylogenetic trees literature - source code Pascal, C, HyperTalk sw requirements HyperCard hw requirements - filename TRNA-SEARCH.HQX update 10-Apr-1991 version 1.0 size 200 k compressed Compactor (self-extracting) ASCII conversion BinHex author Shortridge R. D. (Markiewicz P.) description Identification of tRNA genes and plotting of RNA structure literature CABIOS 2 (1986), 13-17 source code - sw requirements - hw requirements - filename WAYEBOX.HQX update 4-Jul-1991 version 1.1 size 338 k compressed Compactor (self-extracting) ASCII conversion BinHex author Waye M. description Management of storage of DNA, clones, enzymes,etc. literature BioTechniques 8 (1990), 660-664 source code HyperTalk sw requirements HyperCard hw requirements - filename WAYECAS.HQX update 4-Jul-1991 version 1.1 size 105 k compressed Compactor (self-extracting) ASCII conversion BinHex author Waye M. description Management of clones generated by cassette mutagenesis literature BioTechniques 7 (1989), 604-606 source code HyperTalk sw requirements HyperCard hw requirements - The PLOTA protein analysis package of A. Luttke and P. Markiewicz: Each file is about 150k in size in Compactor/BinHex format file name description update PLOTA_AADATA.HQX Sequence editor 23-May-1991 PLOTA_DOT.HQX Dot matrix comparison 23-May-1991 PLOTA_GGR.HQX Secondary structure prediction 23-May-1991 PLOTA_GOR.HQX Secondary structure prediction 23-May-1991 PLOTA_HEL.HQX Helical wheel 23-May-1991 PLOTA_HYD.HQX Hydropathy analysis 23-May-1991 PLOTA_HYD5.HQX Hydropathy analysis (averaging) 23-May-1991 PLOTA_KAS.HQX Chain flexibility and antigenicity 23-May-1991 PLOTA_KKD.HQX Prediction of membrane spanning regions 23-May-1991 PLOTA_POW.HQX Power spectrum plot 23-May-1991 PLOTA_SIG.HQX Signal peptide prediction 23-May-1991 PLOTA_SIM.HQX Dissimilarity plot 23-May-1991 PLOTA_TMH.HQX Hydrophobic moment analysis 23-May-1991 (b) Decoding software filename MACCOMPRESS.HQX update 12-Aug-1991 version 3.2 size 75 k compressed Compactor (self-extracting) ASCII conversion BinHex author Chambers L. description UNIX-compatible compress/uncompress literature - source code - sw requirements - hw requirements - filename STUFFIT_16.HQX update 8-Oct-1990 version 1.6 size 500 k compressed - ASCII conversion BinHex author Lau R. description Installer for latest version of StuffIt Classic literature - source code - sw requirements - hw requirements - filename UNSTUFFITDELUXE.HQX update 8-Jan-1991 version 2.0 size 180 k compressed - ASCII conversion BinHex author Lau R. description Installer for UnStuffIt Deluxe 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 - hw requirements - filename UUD.HQX update 2-Apr-1991 version - size 50 k compressed Compactor (self-extracting) ASCII conversion BinHex author Dumas M. description C source code for UUD uudecoder literature - source code C sw requirements - hw requirements - (c) Other MACREVIEW.1 - Peter Markiewicz's reviews of molecular biology software MACREVIEW.2 available for the Macintosh (Feb. 1991) Files with the extension ".hqx" have to be decoded by (Un)StuffIt or BinHex. 28-Aug-1991