Path: utzoo!attcan!uunet!wuarchive!zaphod.mps.ohio-state.edu!uakari.primate.wisc.edu!caen!uwm.edu!csd4.csd.uwm.edu From: duncan@csd4.csd.uwm.edu (Shan D Duncan) Newsgroups: comp.sys.amiga Subject: Re: Scientific programs on Amiga Message-ID: <6749@uwm.edu> Date: 3 Oct 90 18:17:47 GMT References: <3265.270916da@cc.helsinki.fi> Sender: news@uwm.edu Reply-To: duncan@csd4.csd.uwm.edu Lines: 213 From article <3265.270916da@cc.helsinki.fi>, by ronkko@cc.helsinki.fi: > Here is a list of a few scientific programs I would like to see on Amiga: > > 1) A Bibliographic database (This is a MUST, every scientist need this!) > It has to be flexible and able to communicate properly with other Amiga > programs (Word processing, DTP) > > 2) A multimedia style laboratory protocol book/edatabase/experimet planning/ > report generator/etc./etc. -utility > > 3) Two/Three dimensional drawing tool for biochemical/biological structures > (With animation of course!) > > 4) Genetic sequence analysis (DNA, RNA) softaware (something like PC-gene, but > better!) Not having seen PC-gene but having used a freely distributed program that does do Genetic sequence analysis. I can at least add my: Here is a program that is available and can do what you wish. Anybody want to start a database of sci. programs under various categories such as graphics, output, text, stats, and so forth? Best place would be to skim the fish library and see what you might land. Phylip is a set of programs for doing genetic sequence analysis. Be forwarned that 1) The source and docs are large (about 1 mb). 2) Written in Pascal. I have converted old versions of some of the programs to "C" using the p2C program posted to newxanth and c.b.a/c.s.a. The source is a fairly standard version of pascal but is not as fast as it could be. Joe would REALLY love to have someone run his test data on an Amiga with a pascal compiler. Since I am told every day that molecular biology is the wave of the future I am sure there are thousands, no millions (well maybe tens of thousands) who have been waiting for just this set of programs to fun but did not know about them. Well wait no more! In there somewhere should be a :-) I am sure. Here is Joe's introductory message to phylip 3.3. He does outstanding support!!!!!!!!!!!!!!! From CLASS-L@ccvm.sunysb.edu Tue Jun 12 19:19:26 1990 Received: by csd4.csd.uwm.edu; id AA25727; Tue, 12 Jun 90 19:19:21 -0500 Message-Id: <9006130019.AA25727@csd4.csd.uwm.edu> Received: from SBCCVM.BITNET by ccvm.sunysb.edu (IBM VM SMTP R1.2.2MX) with BSMTP id 0487; Tue, 12 Jun 90 20:19:25 EDT Received: by SBCCVM (Mailer R2.07) id 0413; Tue, 12 Jun 90 20:19:24 EDT Date: Tue, 12 Jun 90 17:09:01 PDT Reply-To: "Classification, clustering, and phylogeny estimation" Sender: "Classification, clustering, and phylogeny estimation" From: Joe Felsenstein Subject: PHYLIP 3.3 Released X-To: CLASS-L%SBCCVM.BITNET@uwavm.acs.washington.edu To: 'Shan Duncan' Status: RO Version 3.3 of PHYLIP, a free package of programs for inferring phylogenies from various kinds of data, was released last weekend. Source code, documentation, and PCDOS executables are available for free from me as usual on diskette, by anonymous ftp from evolution.genetics.washington.edu, by e-mail, or on tape. Below I have appended the PHYLIP general information notice which describes details of distribution. There are many changes from the previous version. Here is a summary of the major changes since 3.2. 1. DNA and protein sequences now input in "interleaved" or "aligned" format instead of all on one sequence followed by all of the next. This means one can more easily use output of alignment programs. 2. The DNA distances program will now bootstrap sequences, and the distance matrix programs will analyze the resulting multiple-data- set input files. Thus one can do bootstrapping on DNA distance trees. 3. A DNA maximum likelihood program assuming a molecular clock is added. 4. Two new interactive menu-driven tree drawing programs are added (the old ones are removed), which allow preview of the trees to be plotted on IBM PC graphics or DEC or Tektronix graphics terminals. They plot to plotters, Postscript laser printers, dot matrix printers. 5. More detection of input file errors, more informative error messages. 6. Programs that infer trees that have branch lengths now print them out in a different format (phenogram-style) that allows approximate branch lengths to be seen. 7. The compatibility program CLIQUE and the consensus tree program CONSENSE now print trees in a more easily interpretable way. 8. Programs printing out hypothetical states at interior nodes now do so in an interleaved format that makes it easier to see all the states of one character as they form a single column. 9. Improvements of the interactive tree rearrangement programs. 10. Correction of a problem in the discrete character programs that had led to them having trouble running even moderate size data sets on PCDOS machines. I will shortly post a notice listing other packages currently available from others. Here is the PHYLIP information sheet. --------------------------------------------------------------------------- PHYLIP - Phylogeny Inference Package (version 3.3) This is a FREE package of programs for inferring phylogenies and carrying out certain related tasks. At present it contains 28 programs, which carry out different algorithms on different kinds of data. The programs in the package are: ---------- Programs for molecular sequence data ---------- PROTPARS Protein parsimony DNAPARS Parsimony method for DNA DNAMOVE Interactive DNA parsimony DNAPENNY Branch and bound for DNA DNABOOT Bootstraps DNA parsimony DNACOMP Compatibility for DNA DNAINVAR Phylogenetic invariants DNAML Maximum likelihood method DNAMLK DNAML with molecular clock DNADIST Distances from sequences RESTML ML for restriction sites ----------- Programs for distance matrix data ------------ FITCH Fitch-Margoliash and least-squares methods KITSCH Fitch-Margoliash and least squares methods with evolutionary clock -------- Programs for gene frequencies and continuous characters ------- CONTML Maximum likelihood method GENDIST Computes genetic distances ------------- Programs for discrete state data ----------- MIX Wagner, Camin-Sokal, and mixed parsimony criteria MOVE Interactive Wagner, C-S, mixed parsimony program PENNY Finds all most parsimonious trees by branch-and-bound BOOT Bootstrap confidence interval on mixed parsimony methods DOLLOP, DOLMOVE, DOLPENNY, DOLBOOT same as preceding four programs, but for the Dollo and polymorphism parsimony criteria CLIQUE Compatibility method FACTOR recode multistate characters ---------- Programs for plotting trees and consensus trees ------- DRAWGRAM Draws cladograms and phenograms on screens, plotters and printers DRAWTREE Draws unrooted phylogenies on screens, plotters and printers CONSENSE Majority-rule and strict consensus trees The package includes extensive documentation files that provide the information necessary to use and modify the programs. COMPATIBILITY: The programs are written in a very standard subset of Pascal, a language that is available on most computers (including microcomputers). The programs require only trivial modifications to run on most machines: for example they work with only minor modifications with Turbo Pascal, and without modifications on VAX VMS Pascal. Pascal source code is distributed in the regular version of PHYLIP: compiled object code is not. To use that version, you must have a Pascal compiler. DISKETTE DISTRIBUTION: The package is distributed in a variety of microcomputer diskette formats. You should send FORMATTED diskettes, which I will return with the package written on them. Unfortunately, I cannot write any Apple formats. See below for how many diskettes to send. The programs on the magnetic tape or electronic network versions may of course also be moved to microcomputers using a terminal program. PRECOMPILED VERSIONS: Precompiled executable programs for PCDOS systems are available from me. Specify the "PCDOS executable version" and send the number of extra diskettes indicated below. An Apple Macintosh version with precompiled code is available from Willem Ellis, Instituut voor Taxonomische Zoologie, Zoologisch Museum, Universiteit van Amsterdam, Plantage Middenlaan 64, 1018DH Amsterdam, Netherlands, who asks that you send 5 800K diskettes. HOW MANY DISKETTES TO SEND: The following table shows for different PCDOS formats how many diskettes to send, and how many extra diskettes to send for the PCDOS executable version: Diskette size Density For source code For executables send in addition 3.5 inch 1.44 Mb 2 1 5.25 inch 1.2 Mb 2 2 3.5 inch 720 Kb 4 2 5.25 inch 360 Kb 7 4 Some other formats are also available. You MUST tell me EXACTLY which of these formats you need. The diskettes MUST be formatted by you before being sent to me. Sending an extra diskette may be helpful. NETWORK DISTRIBUTION: The package is also available by distribution of the files directly over electronic networks, and by anonymous ftp from evolution.genetics.washington.edu. Contact me by electronic mail for details. TAPE DISTRIBUTION: The programs are also distributed on a magnetic tape provided by you (which should be a small tape and need only be able to hold two megabytes) in the following format: 9-track, ASCII, odd parity, unlabelled, 6250 bpi (unless otherwise indicated). Logical record: 80 bytes, physical record: 3200 bytes (i.e. blocking factor 40). There are a total of 71 files. The first one describes the contents of the package. POLICIES: The package is distributed free. I do not make it available or support it in South Africa. The package will be written on the diskettes or tape, which will be mailed back. They can be sent to: Joe Felsenstein Electronic mail addresses: Department of Genetics SK-50 Internet: joe@genetics.washington.edu University of Washington BITNET/EARN: FELSENST@UWALOCKE Seattle, Washington 98195 UUCP: ... uw-beaver!evolution.genetics!joe U.S.A. ***********Now back to our previous poster********************* > > 5) All-in-one file converter utility (Conversion of all major file types from > PC, Mac and amiga to help communication between different Machines; this is a > must!) > > > --------------------------------------------------------------------------- > Reijo Ronkko University of Helsinki, Dept. of General Microbiology, > Mannerheimintie 172, 00300 Helsinki, FINLAND > Fax +358-0-4735426 > > Ronkko@cc.helsinki.fi > ---------------------------------------------------------------------------