DISCLAIMER: The programs listed here were all obtained as public-domain or shareware programs with the consent of the authors. I have not received any compensation, monetary or otherwise, for making these programs available on the Macintosh. If a program is marked as "shareware", you should do the author the courtesy of sending the small registration fee. ************************************************************************** Public Domain/Commercial Program List For Molecular Biology using the Apple Macintosh (April 1990 version) ************************************************************************** Peter Markiewicz MBI (UCLA) 405 Hilgard Ave. Los Angeles, CA 90024 213-825-8924 My internet Address: JMILLER%VXBIO.SPAN@STAR.STANFORD.EDU **************************************************************************** Table of Contents: 1.Notes of the Freeware/ShareWare Programs I distribute: 2.Notes on Getting these Programs by Floppy a)Getting them b)Send extra floppies c)Send me your programs! d)Installation 3.Notes on Getting these Programs by e-mail or FTP from the EMBL,IuBio, me, or Houston-GenBank servers. a) From me via direct e-mail b) EMBL c) IuBio d) Houston GenBank 4.List of Programs available from me 5.List of FreeWare/Shareware/Commercial Programs(not distributed by me) **************************************************************************** 1.Notes of the Freeware/ShareWare Programs I distribute: The I distribute are for the Apple Macintosh, and are of use in molecular biology, biochemistry,and human genetics. I did not write the algorithms used by the programs, and cannot be responsible for their operation. Most of the programs originally ran on IBM PCs, VAXes, or UNIX machines, and were modified to run on the Macintosh. Because these computers are so different in operation from the Mac, many of the programs run in a decidedly un-Maclike manner. One common problem is printing. Many of the programs do not print, or print only to an ImageWriter. These program provide many of the basic analysis routines used by molecular biologists. They are not comprehensive. For example, there is nothing for handling shotgun sequencing projects, or gel digitizer entry of sequences. If you want to use your Mac to do molecular biology, they are a good place to start. They may be all you need, and they will show you what the Mac can and can't do for you. If necessary, you can buy a commercial program later using the knowledge gained from working with these programs. ************************************************************************** 2.Notes on Getting these Programs by Floppy A)The programs may be obtained for free by doing the following: 1. Format (800k) and put BLANK labels on double-sided 3.5 Mac-format disks 2. Enclose them in a package which also includes a stamped (it will need avbout $2.50 US postage), self-addressed envelope. If you are outside the US, you may send international postage sufficient to send back the floppies, the envelope, and about 10 pages of documentation. Note that you will get the programs much faster if you send the envelope with postage on it (weeks) instead of a check for $2.50 (months). If you heard about the programs from someone else, PLEASE GET THE PROGRAMS FROM THEM,RATHER THAN ME. I am a molecular biologist, and I simply cannot handle the hundreds of requests I have received! Distribute the programs to anyone who wants them, rather than having them contact me. If you got the programs from someone else, you can contact me to get on my mailing list. If you are interested in upgrades, write me about a year after you get the programs. B) Extra Floppies: I am not a professional programmer, but a molecular biologist doing this out of the goodness of my heart(!) People often send me the wrong number of floppies, or floppies that are unusable. You can help me by sending 1 or 2 extra floppies to cover this shortfall, which otherwise comes out of my own pocket. C) Send me Your Programs! As mentioned above, all the programs came from other people. If you have a program which might be useful to people on the Macintosh which runs on another computer, and the source code is in the public domain, I am willing to help you convert it to run on the Macintosh. If you don't know what source code is (it is NOT the program on a disk), contact me for an description. Commercial and copyrighted programs cannot be converted! Currently, the most useful programsare those doing multiple sequence alignment, site-directed mutagenesis, and alignment for "shotgun" sequencing. I will look at anything, however. I can work with all languages except FORTH. I also will answer questions from budding Mac programmers about which compilers to buy, utilities, etc. D)Installation: None of the programs are copy-protected, and they do not require any special installation proceedures beyond dragging them onto your disks. MOLGENJR uses additional files in the "files for molgen" folder. ************************************************************************** 3.Notes on Getting these Programs by e-mail or FTP from the EMBL,IuBio, me, or Houston-GenBank servers. An alternate, much more convenient method to get the programs is to send StuffIt-encoded files through e-mail. To do this, you need StuffIt 1.5.1. There are several "server" computers from which you can download the software for free. I can also send you individual programs directly. A) Getting the Programs from me via Direct e-mail 1.Request the programs you want, by name, from this letter 2.When you get the files, download them to your Mac via text kermit. You should have a file readable by a text editor, but full of gibberish. DON'T use the "save stream" option on many terminal programs, as additional characters will be written into the file which will destroy it. 3.Start StuffIt 1.5,and select the "decode BinHex" option to convert the files back to a StuffIt archive. 3.Extract the individual files with the "extract" button. Note that some of the programs are quite big, so they have to be sent individually. I also distribute two info files "Mac in Molecular Biology", which is a review of several commercial programs, and "Compare programs", which is the following summary of all Mac sequence analysis programs available to my knowledge. If you know of others, please tell me and/or send them. Note that most of these programs will be sent to the IUBIO server, the EMBL sever, and the Houston server. Before sending me a list of what you want, you should check these servers. B) The EMBL Server The address of the EMBL server is: "NETSERV%EMBL.bitnet" or NetServ@EMBL-Heidelberg.DE You can send the following command through the mail to reveive a list of mac software: GET MAC_SOFTWARE:filename.ext you can contact a human(Rainer Fuchs) by "FUCHS%EMBL.bitnet" C) The U Houston-GenBank Server The address of the Houston server is: gene-server@bchs.uh.edu (Internet) gene-server%bchs.uh.edu@CUNYVM (BITNET) You should send the word "help" in your subjectto get a help file for this server. like Subject: send mac help For ftp: "menudo.uh.edu" (IP name--the FTP host) 129.7.1.6. (IP address) You can speak to a human (Dan Davidson) by "davison@menudo.uh.edu" D) The IuBio Server The address of the IuBio server for e-mail is: "GILBERTD@IUBIO.BIO.INDIANA.EDU" For FTP, use IuBio is on the Internet network of computers with the name IuBio.Bio.Indiana.Edu (IP name--the FTP host) 129.79.1.101 (IP address) You can also use: ftp.bio.indiana.edu If your computer system is linked to the Internet, it probably has an FTP program. Each FTP program has it's own peculiarities, but most follow a general syntax: ftp iubio.bio.indiana.edu -- connect to iubio user: anonymous password: guest or your real user name (prefered) ? or help -- general help for ftp cd [.subdirectory] -- change directory binary -- use full binary transfer ascii -- use text transfer get any.file -- fetch a file from the archive put my.file -- put a file to the archive (only for [archive.receive] directory) bye -- close the connection The address of the Don Gilbert at the iubio server is: "GILBERTD@IUBIO.BIO.INDIANA.EDU" A more detailed description of the various servers of interest may be found in my HyperCard stack "e-mail info" If you don't feel confident with the above, you can send floppies as described earlier, but be prepared to wait a few months for a reply. When updates or new programs are available,I will post messages. The main reason that I am doing this over e-mail personally is to get back comments, bug reports, source code for new programs, etc., with increased frequency. I will include info on the new commercial servers which have these programs (BioTechNet and America Online) in the future. ************************************************************************** 4.List of Programs available from me. Many of them are available from EMBL, IuBio, or the U Houton gene-server: 1) Basic Molecular Biology Set -- 15 double-sided Floppies DNA ANALYSIS: FORMAT 1.0: The only program in the whole set that I actually wrote! A text editor for DNA sequences, that also provides for re-formatting the sequences into a variety of standard file types, ie., GenBank, NEWAT, EMBL, etc. Mac Compatibility: Works on Mac Plus and up, fine with MultiFinder. OutPut: Can print or save sequences as text files. Graphics: None. Problems: None known, but this is the first release. DNANALYZE 1.8: Provides basic DNA sequence analysis, including Restriction analysis, translation, codon usage, reverse translation of peptide to degenerate oligonucleotide, DNA plots and drawings, gel picture from restriction digest. This is a fairly old (1985) program, about 360k in size. Mac Compatibility: works on all macs except the nex Mac/FX (not practical to make it do so). Runs under multifinder but not "multifinder friendly". Output: Optimized for ImageWriter I and II. Can only print to LaserWriter if printed output is<= one page. Can save results to text file. Graphics: Graphics must be saved by holding down Shift-Apple (cloverleaf)-3 keys, to save as MacPaint file. Only works in monochrome on Mac II. Files: Uses plain ASCII or Bionet format (DNA only). Problems: The COMPARE, Dot-matrix, and open reading frame routines are crash-prone. Use the equivalent routines in MOLGENJR. MOLGENJR 1.2: Provides basic DNA and protein sequence analysis, including restriction analysis, translation, codon usage, also protein analysis of protease cleavage sites, hydropathy, Garnier secondary structure prediction. Also predicts DNA size from gel mobility, radioisotope decay, chemical formulas, etc. This is a fairly old(1985) program, about 360k in size. Mac Compatibility: works on all macs except the nex Mac/FX (not practical to make it do so). Runs under multifinder but not "multifinder friendly" Output: Optimized for ImageWriter I and II. Can only print to LaserWriter if printed output is<= one page. Prints in color using color ribbon on ImageWriter II. Can direct text results to text file. Graphics: doesn't generate screen graphics, makes graph of hydropathy, dot-matrix analysis, or secondary structure prediction on ImageWriter I or II. Files: Uses plain ASCII, EMBL, or Bionet format (DNA only). Problems: Very easy to screw up sequences in the program's text editor. PUPPY: creates a graphical representation of a DNA sequence. Features like palindromes, etc., are much easier to see, and sequence is more compact. Mac Compatibility: works on all macs tested except 128k Output: output to all printers or text file. Graphics: good, can be pasted to ClipBoard Files: ASCII, Bionet, or EMBL Problems: None reported MacDNA II+: Simple PC-style program for various basic DNA sequence manipulations. By Robert Scheif. Mac Compatibility: works on all macs tested. Output: text file only Graphics: none Files: uses ASCII, Bionet, or EMBL. Problems: None reported. DNAID+: Program for DNA sequence analysis,editing, restriction site analysis. Mac Compatibility: works on all Macs tested OutPut: Text/graphics Files: Sequence files, restriction site files Problems: Not extensively tested. LIGATE/CIP: Programs for determining optimum ligation and dephosphorylation conditions. Mac Compatibility: works on all macs tested. Output: text file only Graphics: none Files: no input files. Problems:occasional incorrect tabbing in edit fields. RESTRT: Protram for doing restriction digests of DNA, and graphically representing the results. Mac Compatibility: works on all macs tested. Output: text file only Graphics: good. Files: input files for restriction sites and DNA sequences. Problems: None Reported. MacTargSearch 1.1 (modified from original 1.0 version) Original Authors: James A. Goodrich (designer) Michael L. Schwartz William R. McClure Department of Biological Sciences Carnegie Mellon University Pittsburgh, PA 15213 A program designed to look for sequence motifs in DNA sequences. You create a "target" file, which is a weighted consensus of the sequence you are looking for. At every positon in a target sequence a hierarchy of base pair occurrence is established, based upon an analysis of naturally occurring sites. The program was originally designed to look for E.coli promoters, but can be used for any sequence feature where more than one base is possible at each position. Note: its SLOW. Mac Compatibility: works on all macs tested. Limited mac interface (1.1 better than 1.0). Note: programs may have problems in MultiFinder deleting a scratch file it makes for printing. Output: text file and/or printing. Graphics: none. Files: DNA sequence files, several formats. Program also creates "target" files of a weighted consensus sequence to search the DNA sequence. Can read GenBank,EMBL, DNA Strider files. Problems: None Reported. STADEN--Macintosh version Available 1991 as a commercial program Referenced in CABIOS, vol 6 #4, 1990 The macintosh version of the extremely popular and useful programs in the Staden package are being released as part of a general upgrade of the entire package. The program has a completely rewritten user interface, designed to facilitate porting it to a variety of systems. The best program around for shotgun sequencing projects, gel sequence alignments,building consensus sequences. Can search DNA and protein sequence libraries for sequence "motifs". Works well with very large projects (the paper mentions its use for sequencing Epstein-Barr virus). The program's power and widespread use on VAX systems will probably overcome its somewhat un-maclike interface. 2) RNA Analysis: t-RNA search programs: Search for t-RNA gene sequences in DNA sequences. Draws folded t-RNA structure, which can be printed. Mac Compatibility: works on all macs tested. Output: screen dump of picture of tRNA sequence alignment Graphics: screen only Files: Text sequence files. Problems: None Reported. MULFOLD and LOOPVIEW A pair of programs which allow the user to find possible secondary structures for RNA molecules. Uses extensive energy calculations to arrive at the best structure. May take many hours to run. The results of MULFOLD can be loaded into LoopView to actually see the folded RNA molecule structure. Very powerful. Mac Compatibility: should work on any mac with 1 meg or greater RAM, though MacII is better because calculations take so long to do. Works in backround under Multifinder. Output: text file has numerical values, which can also be read by LoopView to produce a MacDraw-type picture of the folded RNA. Graphics: LoopView only Files: Text sequence files. Problems: None Reported. 3) Plasmid Drawing Programs: MacPlasMap: (new version,1.82) Excellent MacDraw-like program for drawing plasmids with gene regions, restriction sites, and polylinker sequences. Works best when used in conjunction with MacDraw. Best public-domain program available. The author requests a small ($20 US)donation to the following address: Jingdong Liu Biology Department, University of Utah Salt Lake City, Utah 84112 Mac Compatibility: works on all macs tested. Output: text or PICT file, can past plasmid picture to ClipBoard Graphics: excellent, interactive, MacDraw-like Files: plasmid input files (not sequences!). Problems:None reported. PROPLASM: Simple plasmid-drawing program. Mac Compatibility: works on all macs tested. Output: text file only Graphics: primitive Files: program-specific, also can save PICT files. Problems: None reported. 4) Protein Analysis: THREE: Aligns three protein sequences up to 1000 amino acids in length. Mac Compatibility: works on all macs tested. Output: text file only Graphics: none Files: text files in bionet format. Problems: The algorithm can't align sequences which don't share a common N-terminus. AMPHI: Uses hydrophobic moment to predict antigenic sequences in a protein. Mac Compatibility: works on all macs tested. Output: text file only Graphics: none Files: text files in bionet format. Problems: None reported. PLOTA protein analysis package A steadily growing set of programs for analyzing protein sequence. Currently, the package consists of 10 programs (compiled version) or 14 (interpreted versions). A common user interface throughout allows the user to create plots of a protein sequence's hydrophobicity,chain flexibility,secondary structure, and search for motifs like membrane-spanning peptides, leader sequences,and more. The plots created may be printed or exported to MacDraw or a MacPaint-type program. Mac Compatibility: works on all macs tested. Output: text written to disk, copy graphics to ClipBoard or print Graphics: good chart type. Files: reads a variety of sequence file formats. MacPattern MacPattern is a Macintosh application to identify protein sequence motifs and patterns which can utilise the information in the Prosite database (or any other database in Prosite format). Changes in v1.3 include: full MultiFinder support, i.e. works fine in the background now; partial System 7 support (fully System 7-compatible); output can now be sorted by pattern or by location, etc. Mac Compatibility: Works on all macs, good interface. Output: Text output Graphics:In-program,part of interface Files: Reads PROSITE and sequence file formats. 5)Biochemistry Analysis: MacLigand: Used for equilibrium binding studies, does Scatchard analysis Mac Compatibility: works on all macs tested. Output: text file only Graphics: simple Files: no input files. Problems:None reported. Enzyme Kinetics: For simple Michaelis-Menton kinetic analysis. Mac Compatibility: works on all macs tested. Output: text file only Graphics: simple Files: no input files. Problems: None reported. Endocytosis: Mac Compatibility: works on all macs tested. Output: text file only Graphics: none Files: no input files. Problems: None reported. 6) DNA sequence alignment: AlignSeq: Aligns two DNA sequences using techniques of FASTP, from Bruce Roe's lab. Mac Compatibility: works on all Macs tested except 128k. Output:directs output to text file only. Graphics: none. Files: can read EMBL, Bionet, or ASCII format (DNA only). Problems: Program very sensitive to file format, bombs with slight changes DottyPlot: Creates dot-matrix graph of two DNA or protein sequence. Excellent Mac interface, allows saving graphic as PICT file, printing,copying to ClipBoard. Reads files in several common formats (Bionet, GCG, etc.) Mac Compatibility: works on all Macs tested. Small Macs may have problems with graphic display. Output: directs output to all printers, screen, ClipBoard, PICT file. Graphics: Extensive,multiwindow,noneditable. Files: Can read several sequence file formats. Problems: None reported. Ralign: Aligns several DNA sequence accd. to Waterman's algorithm. Reasonable Mac interface. Aligned sequences are not numbered. Mac Compatibility: works on all Macs tested. Output: output into editing window, which can be saved or printed. Graphics:none. Files: Uses a unique sequence file format, all sequences to be aligned in one file. Problems: Program sensitive to sequence format,may bomb if incorrect. 7)Protein Alignment: I will be distributing a version of CLUSTAL specific for the mac in 1991. Doolittle's NEWAT Alignment Package: Align up to 50 protein sequences, construct evolutionary trees for related sequences. Requires >4 megabytes on Mac II with coprocessor only. In current (1.0) release, calculation of branch lengths of evolutionary tree is not supported. Mac Compatibility: Mac IIs with 4 megabytes of RAM or greater. Program is sensitive to sequence file format, and bombs easily. Won't work under MultiFinder with 5 Meg Mac II. Output: directs output to text file only. Graphics: none. Files: ASCII format. Problems: Programs are quite sensitive to input file format, may bomb if nonprinting characters are present in the file. The TREE program does not produce a tree properly for a small (<10 number of sequences). I provide an editor, FORMAT, which makes files usable by NEWAT from your text files, and works as a general-purpose sequence editor as well. It contains the "pretty print" routine MULPUB from the package. 8) Utilities: LibProt: Utility for use with the database search program package FASTA, available from William Pearson. M&M editor: HyperCard text editor for writing lab protocolls, proceedures, etc. Extremely useful. 9)Human Genetics Programs: Chromosome Pictures: Paint-format drawings of human chromosome set. Pedigree analysis: LIPED (VAX version), Note that a Mac version of LINKAGE has been developed by Ken Weeks, and is being distributed by Jung Ott, who can be reached at the following address: College of Physicians & Surgeons Columbia University, Dept. of Psychiatry, Box 58 722 West 168 Street New York, NY 10032 212-960-2504 FAX: 212-795-5886 EARN:BITNET: OTT@NYSPI He distributes a newsletter for linkage analysis. You can get a pedigree drawing program, Pedigree Draw, from the following address: Pedigree/Draw $30 Department of Genetics Southwest Foundation for Biomedical Research P.O. Box 28147 San Antonio, TX 78284 U.S.A. 512-674-1410 Comments or questions to Paul Mamelka at: "paul@darwin.sfbr.org" Pedigree/Draw comprises 2 programs that allow creation,editing, and drawing of genealogical diagrams. Programs use mac interface. Mac Compatibility: works on all Macs tested. Output: pedigree drawings, pedigree records. Graphics:good support for PostScript and fanfold printers,prints large pedigrees on several sheets for easy joining. Files: unique file format, can save drawings as PICT file Problems: non reported 3)HyperCard Stacks: I have several HyperCard Stacks, with the following titles: Materials & Methods Editor (very good) Molecular Cloning DNA Teacher (basic tutorial) Gel Fragment Sizer Buffer Calculations Program list (1991) e-Mail information(1991) ************************************************************************* 5.List of FreeWare/Shareware/Commercial Programs(not distributed by me) This list also includes commercial programs. I do not distribute them, of course (no, I won't pirate a copy for you!) A brief description of the programs is included. Many have been more comprehensively reviewed in "Using the Macintosh in Molecular Biology, the companion message to this one. If you want to contact some of the sources listed here for programs, please CALL them before sending off floppies, etc. I have gotten some irate replies from some of the sources about having the wrong amount of money sent. Protein Graphics: MacImdat $2950 (50% academic discount) Molecular Applications Group,880 Lathrop Drive Stanford, CA 94305 FAX (415)-857-1754 MacImdad is capable of displaying three-dimenstional structures of molecules ranging from small organic molecules to large proteins. It is capable of several display modes, including "ball and stick", dot surfaces, and space-filling display. Can read Brookhaven coordinates for protein structures. Special algorithms developed specifically for viewing protein structures. Extremely powerful, comparable to protein modeling programs available on graphics workstations like Iris and Evans and Sutherland. But you can't replace an amino acid and do energy minimization like you can in UNIX programs like FRODO. Worst mac interface of any commercial program I have ever seen. Program is controlled by typing in commands in a nonscrolling window. Company apparently thinks mac users want character-based UNIX. Programs like InsightII on the Iris have a far superior user interface. Upgrades and online support available for an additional $500/yr. Nothing in its class on the mac. A must buy if you do protein modeling. To make the program run 3-5 times faster (read:not frustratingly slow)you might want to get a speed upgrade for your mac II to a 40mHz Mac f/x(about $2000, from Apple). Mac Compatibility: Mac IIs with 4 megabytes of RAM or greater and large (100meg) hard disk. DOES NOT USE Mac Interface, UNIX-like Output: can copy pictures to PICT files via clumsy method. Graphics: Extremely good, 256-color, 3-dimensional. Files: can read Brookhaven coordinate files MacMimic Instar Software AB Research Park IDEON S-22370 Lund, Sweden sundinKC@dna.lth.se ok2aps@seldc52.bitnet Anders Sundin Demo avail. by FTP from: pollux.lu.se as macmimic_demo.sit.hqx. MacMimic is an application for the display, construction and comparison of molecular models in full 3-D. It runs on the Macintosh II family of computers with a 256 colour monitor and 2 MBytes of memory. A demo of MacMimic version 1.0 is available via anonymous ftp from The Macintosh interface fully implemented, including Undo. Can display and handle structures with up to 32000 atoms.Molecules are displayed as stick or ball-and-stick models, each with toggable attributes such as atom labels, atom index and stereo. individual atoms or whole structures can be painted in any color. Structures can be created in the program, input from the MolLib library of structures, or obtained from a database as a PDB file (Brookhaven Protein Database file) or as an XR file (Cambridge Crystallographic Database file). Structures can also be imported and exported to the Macintosh applications Ball&Stick and Chem3D. MacMimic has a powerful structure editor which can create new and modify existing models. The MacMimic package includes the molecular mechanics program MM2(87). The MM2(87) User's Manual provides a detailed and authorative description of MM2(87). All computational options (for instance dihedral drivers, restricted motion, etc.) of MM2(87) can be accessed through an interactive input interface. MM2(87) can be run as a background task. Mac Compatibility: Mac IIs with 4 megabytes of RAM or greater. Output: high-resolution graphics Graphics: Extremely good, 256-color, 3-dimensional. Files: ????? MacMolecule via anonymous ftp to iubio.bio.indiana.edu, cd [archive.chemistry.mac], get macmolecule.hqx MacMolecule is a free program for displaying space-filling models of molecules up to 1000 atoms. Somewhat slow. Has files included for DNA,RNA and other biological-type molecules. Must explicitly change coordinates by editing the text data file. Brookhaven format not directly accepted, requires some modification. Beautiful output as good as any workstation, may be copied to ClipBoard for pasting into other graphics programs. Good choice for educators and students learning chemistry. biochemistry. DNA/RNA Builder and Protein Predictor $199 for DNA/RNA builder, $299 for protein predictor, Atlantic Software, P.O. Box 299, Wenham, MA 01984 617-922-4352 Programs excellent, user interface fair Two relatively unique programs for molecular biology. DNA/RNA builder allows you to create 3-dimensional models of DNA in various forms (A,B, single/double-strand, no Z-DNA!). Programs creates a picture that may be printed, or a coordinate file that may be uploaded to molecular modeling packages on mainframes/workstations. The program is an easy way to create these coordinate files, and the printed output is very good.The generated 3D structures of DNA can be rotated and viewed from different perspectives. User interface is NOT like a Mac, to put it simply. Protein Predictor allows you to predict hydropathy or secondary structure of a protein sequence. It uses classical parameters for prediction, and new "neural net" algorithm, which results in better predictions of secondary structure. Produces very nice graphs which can be printed or copied to the ClipBoard for pasting into MacDraw and other programs. Again, useful for those working with proteins of unknown structure. Company makes several other programs of interest to those in the biosciences. Mac Compatibility: not a good mac interface Output: 3d plots of DNA molecules Graphics: graphics may be copied to clipboard for use in MacDraw Files: custom sequence file formats Problems: fixed nonmoving windows annoying under MultiFinder 2-Dimensional Molecular Drawings: ChemDraw Cambridge Scientific Computing, Inc of Cambridge, Massachusetts (617) 491-6862. (program excellent, user interface excellent) The program is designed to produce 2-dimensional drawings of organic molecules. It has a MacDraw-like interface for making the drawings, with all common chemical symbols available. Excellent program for this function. Mac Compatibility: Any mac with 1 meg RAM Output: text and graphics,excellent Graphics: very good. Files: unique file format, but can export to MacDraw and other "Draw"-type programs. Additional Chemical Drawing Programs: ISIS/Draw, $495 (mac application) Molecular Design Ltd. 2132 Farallon Drive San Leandro, Calif. 94577 Tele: (415)895-1313 (800)635-0064 Fax: (415)352-2870 "ISIS/Draw" (Integrated Scientific Information System) is available for both IBM/compatible and MAC systems, as well as VAX/VMS and other systems, according to the article. It is supposed to have chemical intelligence that "understands the chemistry behind reactions", and warns the user when valence limits are exceeded. Mac Compatibility: ???? Output: ???? Graphics: ???? Files: ???? *********************************************************************** Comprehensive Sequence Analysis: IBI Mac Sequence analysis programs(MacVector) (program excellent, user interface excellent) $2400,International Biotechnologies, Inc Large suite of programs doing nearly everything you need on the Mac. Very mac-style intutitve user interface. Easiest of the big commercial programs to use. No true shotgun sequence alignment routine, but other alignments available. Program is capable of recognizing numerous input files, including GenBank, EMBL,BIONET, Staden, U.of Wisconsin, and others. GenBank on CD-ROM is supplied. Program can directly search GenBank files for sequences, authors, references, etc. It is very easy to search comments in GenBank or PIR, and extract the sequences for analysis. Reads feature tables and draws their position on the sequence using the "annotated sequence". Numerous DNA and protein sequence analysis routines are present. Graphics are excellent. "Zooming" graphics allow detailed inspection of small portions of the sequence. MacDraw-like tools allow user to draw directly in output windows. Requires a Mac SE or Mac II to run. It won't run on the Plus because it uses a hardware copy protection scheme which plugs a little box into your keyboard. This is the best solution to copy protection I have seen, since it doesn't require a master disk, and unlimited backups can be made. Mac Compatibility: Mac SE or Mac IIs can't use a Mac Plus. Output: text and graphics,excellent Graphics: very good. Files: can read several common sequence file formats. GeneWorks $2400, Intelligenetics, 700 E. El Camino Real, Mountain View, CA 94040 415-962-7300. Another very sophisticated sequence analysis package, using a novel user interface. Very powerful, but requires high-end mac to run acceptably. IntelliGenetics appears to be aiming for a complete sequence analysis environment, including preparing output for publication. No shotgun sequencing alignment functions. Sequence is worked with in a series of interconnected "views",such as text, graphics, comments, analysis, etc. If you click on a graphical representation of a sequence feature (ie., a coding region), the corresponding sequence is selected in the editor. Editing the sequence can automatically update all the analyses. Elaborate desktop publishing features, allowing the user to set up their charts, etc. with data output entirely within GeneWorks. Numerous DNA and protein sequence analysis algorithms are available. Can be set so analysis is updated while editing sequences. EMBL database is supplied on CD-ROM. Can search for sequences, authors, references, etc. Can search sequence databases using secondary structure and hydrophobicity patterns. Requires some learning to use all its features, but the program will satisfy the most demanding of power users. Sequence database functions are very powerful, but difficult to use. Requires a Mac II system to run efficiently, won't run on Plus. Uses a hardware copy protection box you plug into the keyboard. Occasionally slow. Mac Compatibility: Requires Mac II with >= 2megs RAM. Output: text and graphics,excellent Graphics: excellent, can draw on graphics, DTP functions. Files: can read several common sequence file formats. MacMolly Sequence Analysis $1200-$5000, Soft Gene Berlin, Offenbacher Str 5, D-100, Berlin 33 Germany. Intl Phone: #030/821-1407. (programs excellent, user interface OK) Write to above address for pricing and order forms. Currently the best choice for labs doing a large "shotgun" sequencing project, building a consensus from gel sequences. The first, called MacMolly's "Heart", contains several programs for analysis of DNA and protein sequence analysis. It is the only game in town for doing comprehensive shotgun sequence alignment. "Zooming" graphics like other commercial programs. The programs usually use the mac interface, but sometimes has strange menu commands (you must select several menu commands to make anything happen). Good routines for finding open reading frames in a sequence, and selecting them for copying, saving, translation, etc., with a mouse. Graphics and printing not as good as other commercial programs. Graphics often cannot be printed or copied to ClipBoard. Might be good to use its powerful routines in conjunction with the graphics in DNA Strider. Sequence databases available on CD-ROM. Not copy-protected. Runs on Mac Plus and newer machines. New versions print with LaserWriter. If you have an old version of this package, get the upgrade by all means. Program is now distributed by DuPont with their automated sequencing system. Mac Compatibility: Mac Plus to Mac II,interface a little quirky. Output: text and graphics,excellent Graphics: very good. Files: can read its internal file format, import/export text files. DNA Strider(new 1.1 version) $200 US, Christian Marck, Service de Biochimie, Batiment 142, Departement de Biologie, Centre d'Etudes Nucleaires de Biologie, 91191 Gif-sur-Yvette Cedex, France. (program excellent, user interface fantastic) Fantastic user interface, one of the best I have seen on any mac program, and better than any other sequence analysis program available for its price. Has extremely powerful sequence editor (no digitizer input). Very fast restriction maps, with high-resolution graphics. Has the best sequence editor of any program except possibly MacVector. New version allows saving results as PICT or TEXT, ability to read several sequence formats, and multiple genetic codes. Upgrade in 1990 will add database searching. Old version, was free, lacked these routines. The new version costs $200 US, and is well worth the asking price. Christian Marck has also promised upgrades to those who buy the new version of this program. Mac Compatibility: Mac Plus to Mac II. Output: text and graphics,excellent Graphics: very good. Files: can read its internal file format, import/export text files. The DNA Inspector IIe $295, TEXTCO, 27 Gilson RD, West Lebanon, NH 03784 (603)-643-1471 (program good, user interface good) General DNA sequence analysis (limited protein analysis). Available in several versions since 1984, and has few bugs. Has shotgun sequence alignment routine. No digitizer input. Individual routines are fast, but moving between different menu options is very slow. Allows import of GenBank files. Handles ambiguous nucleotides. Doesn't do sequence database searches. Good user support from company. I rank it high because it has been around a long time, has a easy-to-use if slow user interface, and good support for Laserprinters. It is NOT powerful enough to manage a big shotgun sequencing project, or one that requires sequence database searches and multiple sequence alignment. Runs on everything except 512K Macs. No database searches. Demo version of program available. Copy-Protected. Mac Compatibility: Works on all macs with >= 1 meg RAM Output: text and graphics saved or printed Graphics: confined to single page the size of a small mac screen Files: internal format, can read text sequence files Problems: none reported to me for current version. GeneJockey Biosoft 22 Hills Rd Cambridge, CB2 1JP, UK Price ~ $500 US Commercial program comparable in features and power to DNA Strider, and shows the same intelligent interface design. Supports multiple genetic codes. Can search sequence and/or comments of a DNA sequence database, with wildcard searches possible. Can output a variety of sequence file formats to other programs, but only reads text and DNA Inspector input files. No protein analysis functions except for hydropathy plot. Nice sequence alignment feature. Supports a communication window for connecting to a VAX or other computer via modem. Demo version of the program is available from Biosoft. Runs on Mac Plus and greater. Mac Compatibility: Works on all macs with >= 1 meg RAM Output: text and graphics saved or printed Graphics: confined to single page the size of a small mac screen Files: internal format, reads text and DNA Inspector, outputs several formats. Problems: none reported to me for current version. Applied Biosystems Sequence Analysis Package (no address) A set of program for use in conjunction with the AB automated DNA sequencer. The programs can directly record and analyze sequence data from the sequencer. Another program does an excellent job with aligning sequences from shotgun sequencing projects. The alignment routines are the best for sequencing projects on the macintosh. No analysis routines (secondary structure, translation) available. Output: ???? Graphics: ???? Files: ???? Problems: ???? ******************************************************************* Sequence Database Searching: GenBank Sequences GenBank, c/o Intelligenetics, 700 E. El Camino Real, Mountain View, CA 94040 415-962-7300 $125 - $175 depending on disk format, and method of payment. Pearson's sequence analysis package (see below) uses GenBank files directly, and you will have to get them to do searches with his programs. GenBank can be obtained on tapes, CDROM or floppies for very reasonable prices. Call 415-962-7364 for details, or send a mail message to genbank@genbank.bio.net. Pearson FASTA Sequence Analysis Programs $60.00 for program set. $75.00 for protein library add $20.00 if ordered with P.O. Note: You will also need to get GenBank sequences (see above address). William R. Pearson1611 Westwood Rd., Charlottesville, Va 22901 (804)-924-2818 (programs excellent, user interface fair) Program set (FASTA, Sindex, etc) allows rapid search of GenBank, PIR/NBRF, or user-generated DNA and protein sequence libraries for matches to your sequence. Good alignment routines. Programs capable of things like translating GenBank DNA sequences to protein on the fly, and comparing it to you protein sequence. Very fast algorithm, now used by all commercial packages. NOTE: I USEDTO DISTRIBUTE AN OLD VERSION OF FASTP. I NO LONGER DISTRIBUTE IT, AND YOU CAN ONLY GET THESE PROGRAMS FROM WILLIAM PEARSON! These are more recent versions of the programs I used to distribute, and have many more features . Get them! Program have UNIX-style user interface, but they get the job done. Until programmers take the trouble to build Mac interfaces on their programs, we will have to contend with PC or UNIX-style operation. Programs saves alignments as disk files. Can save graphics as MacDraw-type files. Very good, but remind the author that a more Mac-style user interface would increase their use and his market. Not copy protected. Should run on all macs. Mac Compatibility: Limited use of mac interface Output: text and PICT graphics Graphics: simple PICT graphics Files: "pearson format protein sequence files" Problems: ???? MacPattern free,via e-mail or ftp from the EMBL server, Rainer Fuchs EMBL DATA LIBRARY THE EMBL SERVER; NETSERV@EMBL send an e-mail message with the following message (no comment line) GET MAC_SOFTWARE:filename.ext GET MAC_SOFTWARE:MacPattern.hqx (Program excellent, user interface fantastic) Program allows you to search the PROSITE database of protein sequence motifs with a test protein. For example, if you have an unknown protein, searching with MacPattern may reveal iron-sulfur clusters, poteintial leucine zippers, and so on. Program is very maclike and is easy to use. The prosite database is also available from the EMBL server. "Four Stars" for this excellent program. Runs on Mac Plus and above, not copy protected. Mac Compatibility: runs on all macs,nice interface Output: text results,save test sequences,patterns Graphics: some Files: uses PROSITE database Problems: ???? GenBank Search (HyperCard) Available via anonymous FTP; Iubio.Bio.Indiana.Edu, cd [archive.molbio.mac], (see ftp notes,above) get using ftp from the IuBio server with Get GBSearch.Hqx. The GenBank Search is a Macintosh Hypercard stack for interacting with the computer services of GenBank, the molecular biology databank over electronic networks like BITNET and InterNet. It allows you to search the current GenBank databank for similarities with a query nucleic acid or protien sequence of yours, and get a sequence in the current GenBank by locus name or accession number. The program allows the user to retrive sequences from the various servers mentioned above without the trouble of learning the arcane,character-driven world of mainframes. Mac Compatibility:Should work with any Mac that can run HyperCard. Needs --a Macintosh that is connected to the national Internet network, thru an Appletalk or Ethernet cable, --MacTCP communications software, and Hypercard version 1.2 or later, from Apple Computer, --a valid Internet return mail address. Graphics: nice interface Files: retrives files from remote servers Tour of the Internet available via anonymous ftp on: nnsc.nsf.net, directory internet-tour filenames and The NSF Network Service Center (NNSC) has developed a Tour of the Internet in HyperCard (TM) format for novice network users. The stack has basic information including history, sample email, ftp, and telnet sessions, and a glossary. The Tour is intended to be a fun and easy way to learn about the Internet. A "Local Info" section is part of the Tour. This section is a place where an organization can add information relevant to its own group of users, for example a listing of resources at that site, or other, specialized information. The stack uses HyperCard 2.0 (TM) which requires Macintosh system software version 6.0.5 or higher. The files have been compressed using StuffIt 1.5.1 and take up about 760k when converted to their original format. ******************************************************************* Software for submission of sequence data to EMBL/GenBank/PIR: AUTHORIN Free, GenBank c/o IntelliGenetics, Inc. 700 East El Camino Real Mountain View, CA 94040 415-962-7364 FREE Program for editing your sequence data for submission to GenBank databanks. Converts your sequence to the proper form, provides annotations, feature tables, etc. When the sequence is converted, it may be submitted to GenBank via mailing floppies or electronic mail. New 2.0 version available, much less buggy. A must if you plan to submit sequences to GenBank. Could use an export function so sequences could be typed in using AUTHORIN, and exported to analysis programs. Mac Compatibility: should work on all macs Output: creates submission form Graphics: in interface. Files: can import sequence files. ********************************************************************* Computer Aided Vector Design (CAD) Gene Construction Kit $895 ($495 academic) TEXTCO, 27 Gilson Road, W. Lebanon, NH 03784 (603)-643- 1471 Available summer 1989 Program fantastic User interface Fantastic This program is essentially computer-aided design (CAD) for cloning projects. The program allows you to manipulate DNA sequences either directly through an editor, or indirectly through a drawing of the DNA complete with restriction sites, genes, etc. To do computer cloning, one simply drags a fragment from one plasmid picture to another. It is like having MacDraw pictures of your genetic constructs, but having the underlying DNA sequence directly connected to the various restriction sites and genetic regions. The program 'remembers' previous constructs. For example, if you construct a new vector by fusing several sequences in separate cloning experiments, you can look at previous incarnations, and even arrange them in a "history" window. There is also a "Layout" window, which allows you to arrange the pictures of your construct with text and additional graphics (in short, a desktop publishing window). This program is fantastic. If you can afford it, and are doing vector construction/cloning, you MUST get the program. It is exactly the program with which to blow away your PC friends, since nothing like it exists anywhere short of IntelliGenetic's StratGene $50,0000 expert system! It is by far the better deal! Showing this program off on a Mac II would be a good way to convince hostile co-workers to allow more macs in your department. Mac Compatibility: Mac Plus to Mac II. Output: text and graphics,excellent,groundbreaking Graphics: very good,groundbreaking. Files: can read its internal file format, import/export text files. CAD Gene Genetic Technology Corporation P.O. Box 1179 Kendall Square Cambridge, MA 02142 800-462-7179 508-879-0258 Price ???? Commercial program for computer-aided vector design. Allows managing nucleotide sequence and associated site data in a interactive graphic representation. Links graphic representations of restriction maps and sites (ie., open reading frames) to the underlying sequence. Unlike Gene Construction Kit, program can directly read GenBank files and their feature tables. This means the program will automatically note the positions of reported genes, promoters, binding sites, etc. Has a substantially different interface for Gene Construction Kit Good routines for working with restriction data. Allows computer cloning of sequences, keeping track of "sticky" ends. A Genealogy database keeps track of the history of a sequence construct. Has speech synthesizer for entering and reading sequence data, supports some tablet digitizers. Demo version available. Mac Compatibility: Mac Plus to Mac II. Output: text and graphics,excellent,groundbreaking Graphics: very good,groundbreaking. Files: can read its internal file format, import/export text files in GenBank, NBRF, and other formats. MacPlasMap Jingdong Liu Dept. of Biology University of Utah, Salt Lake City, UTAH, 84112 801-581-6307 (program excellent, user interface excellent) EXCELLENT program for creating plasmid maps. Allows MacDraw-like interaction to create restriction sites, gene regions, polylinker regions, etc., on circular plasmids. Some features handled through dialog windows may be done entirely by mouse in later versions. Excellent LaserWriter output, and the Copy command puts the complete map into the ClipBoard for use in other "Draw" programs. It also can save a MacDraw PICT file of the plasmid picture directly. User must know numerical positions of restriction, polylinker sites, as there is no function in the program which will find restriction sites in a sequence. Only the picture and associated comments is present in the output file, rather than the DNA sequence itself. The best noncommercial plasmid drawing program by a mile! Mac Compatibility: Mac Plus to Mac II. Output: text and graphics,excellent Graphics: very good. Files: can read its internal file format, import/export text files. Plasmid ARTIST v. 1.1 $395 plus 7% sales tax, $5 shipping(California), GeneSystems Computer Software, 755B Loma Verde Avenue, Palo Alto CA 94303 415-493-0972. (program excellent, user interface excellent) Commercial Plasmid drawing program, MacDraw-like interface. Allows several text styles, custom arrows. Appears to call PostScript directly, which allows smoother shading and curves than from programs making QuickDraw pictures. Also appears to have some page layout capabilities like desktop publishing programs. Somewhat expensive for a single-purpose program of this type, but more powerful and easier to use than MacPlasMap. Mac Compatibility: all macs Output: can copy pictures to PICT files Graphics: very good Files: ???? ********************************************************************** Oligonucleotide/PCR Design: Primer (operating license required, no commercial use) C source code available via anonymous ftp from genome.wi.edu For information on Macintosh version, retrieve the readme.asc file from the /distribution/primer.0.4 directory. (Whitehead Institute in Cambridge, Mass) Macintosh, IBM-PC, and Sun executibles are available. Note the Macintosh version is not a Macintosh interface, rather its just a TTY window on the Macintosh and looks just like the Unix, PC, or VMS versions. A complete manual is also available. OLIGO National Biosciences, 725 Tower Drive, Hamel, MN 55340 612-478-6626 FAX:612-478-2375 Commercial program for analysis of primer sequences. Capable of the following analyses: optimal primer pairs for PCR,find oligos that don't form hairpins,optimal hybridization temperatures, optimal annealing conditions for PCR,correct for salt/formamide concentrations, find false priming sites and palindrome sequences,calculate all thermodynamic parameters for duplexes,works with ambigous base symbols for DNA and RNA,compatible with most sequence file formats. Mac version to appear late in 1990. Mac Compatibility: ???? Output: ???? Graphics: ???? Files: ???? Problems: ???? ********************************************************************** RNA Structure Analysis: MULFOLD, and LoopView, free, available via ftp from the IuBio server programs for predicting and drawing RNA secondary structures. Available for anonymous ftp: ftp iubio.bio.indiana.edu user: anonymous cd [archive.molbio.mac] get mulfold.hqx or get loopview.hqx MulFold is Don Gilbert's Macintosh port of MFOLD, software for prediction of RNA secondary structure by free energy minimization, version 2.0 including suboptimal folding with temperature dependence, by Michael Zuker and John Jaeger(Science, 244, 48-52, (1989);Proc. Natl. Acad. Sci. USA, BIOCHEMISTRY, 86, 7706-7710, (1989)). This version is limited to 300 bases per folding, and requires 1 megabyte of free memory to run. It should operate on a Mac Plus, but a Mac II or better is suggested due its time-consuming calculations. MulFold will operate in the background under MultiFinder so that your Mac is useful for other things during the several hours MulFold may be running. This program is a hybrid of the original VMS-Vax program and Macintosh user interface. The .CT output files may be viewed directly with LoopViewer (available in the same ftp directory as loopviewer.hqx). LoopViewer FREE, Drawing RNA secondary structures. Companion program to MULFOLD. LoopViewer accepts data CT (connect) file format,produced by Micheal Zuker'MulFOLD programs, and the format for Gary Olsen's LOOPSOL program. Requires MacII with coprocessor to run (no Mac Plus/Se/Classic/LC). LoopViewer is a subset of a more complete RNA structure drawing and editing program, LoopDLoop. As of this writing, the complete LoopDLoop is still under development. Mac Compatibility: Mac II with lots of RAM, runs in bkgnd under Multifinder during long calculations. Requires MacII with coprocessor to run. MULFOLD runs in backround under MultiFinder. Output: MULFOLD outputs text,used by LoopView to do graphics Graphics: very good(Loopview). Files: can read its internal file format *********************************************************************** Entry of Sequence Data from Gels: DNA Parrot Gel Digitizer System $700, TNT Research, 44 George St. Etbicoke, Ontario, CANADA M8V2S2 416-252-4789 Voice recognition module about $800 System consists of ÒDNA ParrotÓ software, (now a desk accessory), and a hardware gel digitizer box and mouse. If you are willing to spend some money, you can also get voice recognition hardware, which will allow you to read off the gel without typing to your mac. The box plugs into the serial port of the Mac, and a cable connects the 5-button mouse. The user positions the mouse over the gel band, and clicks the keys corresponding to the base (it ispossible to enter ambiguous bases). The keys light up when clickes,and the Mac says the base name in a male and female voice, flashing the key lights. If you have the voice recognition, you simply say the bases as you read them. A simple solution to sequence entry that works well. It is much less expensive than ÒsonicÓ digitizers, which can run $3000-$4000(!) Mac Compatibility: Mac Plus or greater,System 6.04 or later voice recognition requires extra hardware. Output: text files with sequence Graphics: none. Files: can read its internal file format,makes text files Problems: New DA version nearly bug-free, fast. SeqSpeak 1.0 free from IuBio archive via anomyous ftp, at iubio.bio.indiana.edu, in the [archive.molbio.mac] sub-directory. If you don't have ftp, contact Kenneth Connover at:kconover@ac.dal.ca A HyperCard based DNA sequence editor for the Macintosh. It speaks the bases as entered from the keyboard. Keyboard can be configured to correspond to the order of the sequencing reactions on the gel. An entered sequence can be spoken back for confirmation. Sequences can be saved in a number of different formats, making it easy to move the data between different programs. Mac Compatibility: Mac Plus or greater,System 6.04 or later and HyperCard 2.0. Output: text files with sequence Graphics: none. Files: makes text files in several formats Problems: unknown. ******************************************************************** Biochemistry: k.cat $395.00 (academic), BioMetallics, P.O. Box 2251, Princeton, NJ,08543 (609)-275-0133;(800)-999-1961,FAX: (609)-275-9485 Commercial program for analysis of enzyme kinetic data,full-featured Does nonlinear regression on Michaelis-Menten equation under several inhibition conditions. Allows differentail weighing of data point outliers. Has editing and merging functions, Produces output in form of reports or plots. A second program, deltasoft does ELISA analysis, and its data is compatible with k.cat. Mac Compatibility: ???? Output: ???? Graphics: ???? Files: ???? Problems: ???? KINETIC_MODELLER described in Hargrove et al. (1990),BioTechniques 8:1-6 $25,Available from the Biological Sequence/Structure Computational Facility (BS/SCF) University of Georgia Research Foundation, Cosmic Program 382 E. Broad St. Athens, GA 30602 for $25, or Dr. Hargrove in Food and Nutrition, University of Georgia, Athens, GA OR This program models gene expression. Mac Compatibility: ???? Output: ???? Graphics: ???? Files: ???? Problems: ???? ****************************************************************** Communications: HyperFTP Patched version 1.2, as a BinHex encoded, Stuffit file, via anonymous ftp to Iubio.bio.indiana.edu, directory [archive.util.mac] as HyperFTP.Hqx. There is a new version of the easy-to-use HyperFTP hypercard stack by Douglas Hornig. This stack does file transfers to and from your networked Macintosh to other computers, especially archive computers like the Iubio biology archive, or the Info-mac archive at Sumex-aim.stanford.edu. To use this, your macintosh needs to be connected via Appletalk or Ethernet to the Internet, and it needs to have the MacTCP network software from Apple installed. Mac Compatibility: ???? Output: ???? Graphics: ???? Files: ???? Problems: ???? Usenet News reader for Macintosh Available via FTP to SUMEX-AIM as follows. $ tcp sumex-aim 36.44.0.6 sumex-aim.stanford.edu sumex.stanford.edu TheNews can be found in the directory /info-mac/comm and it is called The-news.hqx and is roughly 200K and the .SIT file is 145K Program similar in intent to HyperFTP, allows you to communicate with remote servers via a friendly HyperCard interface. Mac Compatibility: Mac plus or greater Output: ???? Graphics: ???? Files: ???? Problems: ???? MacWorkStation--GCG Programs Front End (No availability information yet) A "front end" is a program that runs on your mac, and handles interaction with a less friendly program on a host computer like the VAX. In the near future, there will be a front end program for interacting with the GCG suite of programs: It's based on Apple's MacWorkstation, a data exchange software for VAXes and Macs. MacWorkstation provides a well-defined protocol for data exchange between these machines. You can write Mac-like programs on the Vax (i.e. programs containing toolbox calls) and the Mac-specific commands are transferred to the Mac and executed there. Based on MacWorkstation, Will Gilbert developed some software to access VAX software packages. At the moment his program supports the PIR programs,programs developed at Whitehead, and some of the GCG programs (those without graphics output). He talked to GCG and they promised to develop PICT drivers for the GCG package to be able to run programs with graphics output as well. In practice, you have a menu with the programs available, and after selecting one you'll get a dialog for setting up the parameters. This is all driven by a VAX program! Then the selected program is executed on the VAX and the results are displayed in a Mac window. Handling of these windows seems to be the only part actually done by the Mac. Mac Compatibility: should work on all macs Output: allows interaction with a remote computer Graphics: PICT drivers Files: ???? Problems: ???? ****************************************************************** Other Programs: Image (1.33) FREE, by Wayne Rasband(NIH), available via anonymous FTP from alw.nih.gov in the directory /pub/image. Image is a program for analysis of gray scale pictures of all types. Its chief lab use is for densitometric quantitation gels. For example, one could use a polaroid negative taken of a ethidium stained agarose gel, scan it into the mac using a scanner or TV camera, and quantify the results. It uses greyscale, so you will require a Mac II displaying at least 256 colors/greys, more than 1 meg RAM, and a scanner or video capture board. Image is even capable of controlling the capture board! The program allows one to take a known grey scale output (using a Kodak step tablet negative for example) and map this to the output of the camera that you are using. The program has an impressive list of abilities for manipulating and quantifying greyscale images. Image can adjust contrast, cut and paste gel lanes, do false coloring for detection of faint bands, and turn negatives into positives. It comes with a well written and illustrated manual, and source code (Pascal). Mac Compatibility: should work on mac II with >=256 colors Output: images,variety of formats Graphics: extensive Files: ???? Problems: ???? Recombinant DNA Management Stacks $10.00,Mary Waye MRC Group in Peridontal Physiology University of Toronto 4384 Medical Science Bldg. Toronto, Ontario, M5S 1 A8 CANADA A set of HyperCard Stacks for managing locations of restriction enzymes and recombinant clones. Works as a set of HyperCard stacks, shows graphic pictures of the freezers, lab benches, etc., where things are stored. Maps are arranged in a point and click order, first a picture of the lab, you select5 a freezer, select a box, then data/references/restriction map, and related sequences. Will require modification of the stack pictures/HyperTalk to adapt to your own lab. Mac Compatibility: ???? Output: ???? Graphics: ???? Files: ???? Problems: ???? Chemical Inventory 2.01 (Hypercard 2.0) Dr. Daniel J Swartling Internet: djsx@midway.uchicago.edu The Ben May Institute Compuserve: 71620,1300 The University of Chicago America Online: CHEMSTUD 5841 S Maryland Ave, Box 424 ACS Organic BBS: DASTMAN Chicago, IL 60637 Applelink: DSWART Genie: D.SWARTLING1 This stack keeps track of a lab or stockroom chemical inventory and it will do a full chemical sort of entries, ignoring numbers and prefixes. It includes fields for compound name,formula, molecular weight, company name, catalog no.,where kept, how much on hand, date reordered, commments, and if it is organic or inorganic. It will show the number of organics, inorganics, and total number of compounds. It will print reports using two templates: short-form (name,location, amount) and long-form (name,company,catalog no., location, amount). It comes with its own font- TimesMol- a laser font - and is shareware. Mac Compatibility: requires HyperCard 2.0 Output: ???? Graphics: ???? Files: ???? Problems: ???? RI Manager software and database available by e-mail from gene-server@bchs.uh.edu or netserve@embl.bitnet or by mail from the author. Kenneth F. Manly,Roswell Park Cancer Institute Carlton at Elm Streets, Buffalo, NY 14263 (716) 845-3372 cammanly@ubvms.bitnet or cammanly@ubvms.cc.buffalo.edu K.F. Manly and R.W. Elliott, RI Manager, a microcomputer program for analysis of data from recombinant inbred strains. Mammalian Genome 1: 123-126 (1991). RI Manager is a Macintosh program which helps analyze the results of genetic mapping experiments using recombinant inbred strains. It is a specialized database program which allows easy storage, retrieval, and display of information from such experiments, but it also has tools for statistical analysis of the experimental results. RI Manager is distributed with a database, compiled by Dr. Rosemary Elliott, of over 1000 strain distribution patterns from six sets of recombinant inbred mice. The distribution also includes a user's manual in the form of a self- displaying DocMaker document. The distribution consists of four files: rimgr.readme, rimgr.hqx, ridata.hqx, and ridoc.hqx. The readme file is small and uncompressed; the others are each 110K to 180K and must be converted and unstuffed with Stuffit 1.5.1. Mac Compatibility: Mac Plus or newer (IIfx not tested) Output: Tables of genetic loci with strain distribution patterns, linkages, confidence intervals, references and comments. These tables can be viewed, printed, or copied to other documents. Graphics: Produces graphic genetic map which can be pasted into other programs or printed. Files: Reads and writes either its own format or tab- delimited text files. Problems: The current version can handle no more than 32 strains in a set of recombinant inbred strains. An new version is being tested (version 2, available 6/91) which will remove that limitation and which will allow information from different sets to be merged and analyzed together. MacMul and GraphMu MacMul and GraphMu are multivariate analysis programs for the Macintosh. Manuals and the programs are freely available by anonymous FTP to biomol.univ-lyon1.fr (134.214.100.42) under the form of Word 4 documents, either in macbinary format (in/pub/mac/macmulti/macbin) or in compressed and binhexed format (in /pub/mac/macmulti/h} Word Processor Dictionaries for Bioscience Scientific Software 17 Country Squire Ct St Louis, MO 63146 (314) 993-8586 Software consists of dictionaries that can (only) be used with MS-WORD. Saves having to constantly tell your word processor what words like "DNA" and "genome" mean. Mac Compatibility: Requires MS-WORD Output: N/A Graphics: N/A Files: N/A Problems: ???? References and Conferences on Genetic Engineering BiLine Associates, 2 Fairlawn Lane, Troy NY 12180 , phone (518)271-8306. (H. R. Bungay ) You may order either "BASIC Environmental Engineering, Text & Disk with 80 Programs" for $24.50 plus $3 shipping or BASIC Biochemical Engineering, Text & Disk with 75 Programs" for $30.00 plus $3 shipping. Both come with a 5 1/4" MS/DOS disk for IBM or compatible with graphics card. You may order an additional 3 1/2" disk for $4, Commodore Amiga $4, or Macintosh (preliminary) $2. The programs have indeed been placed in the Public Domain, but the books contain detailed instructions and are essential for maximum use. Mac Compatibility: ???? Output: ???? Graphics: ???? Files: ???? Problems: ???? ************************************************************** PROGRAMS for Phylogenetic Analysis PAUP 3.0 David L. Swofford Illinois Natural History Survey 607 Peabody Dr., IL 61820 program for general phylogeny analysis,similar to PHYLIP. Program output is compatible with MacClade. Faster than PHYLIP. PHYLIP (3.4) in directory "pub" in the ftp area of computer "evolution.genetics.washington.edu" (IP number 128.95.12.41) This is a FREE package of programs for inferring phylogenies and carrying out certain related tasks. At present it contains 31 programs, which carry out different algorithms on different kinds of data. This is not a sequence alignment package, and the user must understand phylogenetic analysis to use it effectively. Among the functions offered are: protein and DNA parsimony, maximum likelihood, distance matrix analysis, continous character analysis, discrete state data (Wagner), and plotting of evolutionary trees. at present, it is available as self-extracting archives from the above ftp source. In very wide use on a variety of computers. MacClade Wayne P. Madison and David R. Madison Distributed by Sinauer Associates, Inc. 413-665-3722 Program for display of phylogenetic trees, MacDraw- like interface. Anyone working with phylogeny should get this program. ************************************************************** PROGRAMS FOR Human Genetics The availability of LIPED and LINKAGE was mentioned above. The VAX-format version of LIPED may be obtained from me with the public domain sequence analysis software, on request. LINKAGE is available from Jung Ott, at the following address: College of Physicians & Surgeons Columbia University, Dept. of Psychiatry, Box 58 722 West 168 Street New York, NY 10032 212-960-2504 FAX: 212-795-5886 EARN:BITNET: OTT@NYSPI Human geneticists would also be interested in HMGL, which can be obtained from the following address: Yale HHMI Human Gene Mapping Library 25 Science Part New Haven, CT 06511 BITNET:GENEMAP@YALEVM FAX:(203)-786-5534 HMGL is the mac version of the human genetic map database, with one file for each chromosome. It is well done, compiled by nomanclature,chromosome, and DNA committes of the Human Gene Mapping Workshops coresponding to the tables as printed in the HGM10 Publication:Volume 51, Numbers 1-4 of Cytogenetics and Cell Genetics(1989) and available free from the Human Gene Mapping Library. Data regarding probes and polymorphisms on the diskettes, as compiled by the DNA Committee, are also contained in the PROBE and RFLP components of the HGML Database. Several fields on the diskette contain pointers to specific records in these components, as described below. References to published literature on the diskettes consist of a five character LIT Ref file number, which point to one of the 13,000 literature citations catalouged in the LIT component of the HGML database. For comments, questions, or copies of the diskettes in other formats, contact Dr. Kenneth K. Kitt at the above address, or at Dept. of Human Genetics Yale School of Medicine 333 Cedar St. New Haven, CT 06520 BITNET:KIDD@YALEMED FAX:(203)785-6568 Pedigree/Draw An excellent and well supported pedigree drawing program for the Macintosh is "Pedigree/Draw 4.0". It provides a MacDraw-type interface and output for doing pedigrees. It is more a visual tool than a database. You can find the current status of this program from: Bennett Dyke at: Population Genetics Laboratory Department of Genetics Southwest Foundation for Biomedical Research San Antonio, TX 78284 or contact Paul Mamelka at "mamelka@uthscsa.bitnet" ********************************************************************** Educational: Inexpensive biological software for the Mac is available from Intellimation Library for the Macintosh, Dept YAH, POB 1922, Santa Barbara, CA 93116-1922. Phone 1-800-346-8355. Most programs are less than $50 and lab pack prices are available. 60 day trial, etc, etc.... ********************************************************************** STADEN-Mac - To be released in 1991, basically a port of the new 1990 version of STADEN. Sacrifices some of mac interface in order to run on on different types of computers with minimal modification. Most powerful routines for managing a large sequencing project of any program available.