From bronze!sol.ctr.columbia.edu!spool.mu.edu!uwm.edu!bionet!WSUVMS1.CSC.WSU.EDU!THOMPSON Mon Jan 13 16:02:10 EST 1992 Article: 1848 of bionet.software Path: bronze!sol.ctr.columbia.edu!spool.mu.edu!uwm.edu!bionet!WSUVMS1.CSC.WSU.EDU!THOMPSON From: THOMPSON@WSUVMS1.CSC.WSU.EDU (Steve Thompson: VADMS genetics) Newsgroups: bionet.software Subject: genetic linkage mapping---summary compilation (long) Message-ID: <920113125151.202002c5@BOBCAT.CSC.WSU.EDU> Date: 13 Jan 92 20:51:51 GMT Article-I.D.: BOBCAT.920113125151.202002c5 Sender: daemon@genbank.bio.net Distribution: bionet Lines: 428 Dear Bio-Soft land networkers: Many grateful thanks are extended to all you classical genetics types who sent me messages regarding my request for linkage mapping software. The response was quite impressive and my associate and myself are most appreciative. As promised, a summary of the replies to my query (repeated below) has been compiled and comprises the following text: my initial query---------------------------------- Fellow netters: An associate of mine is interested in constructing primary linkage maps of Mendelian genetic markers in sheep. She needs to be able to analyze the segregation of dominant, recessive and co-dominant traits in known pedigrees and experimental crosses. She has brought the commercial package Mapmaker from Whitehead Institute to my attention. It appears to be able to do exactly what she needs, however, it reguires the fancy integrated, graphical operating system SCO "Open Desktop." We are curious to find out if there is a less exorbiant alternative available. Has anyone out there heard of any similar mapmaking software with these type of capabilities but designed to operate under either standard DOS or VAX/VMS? Naturally public domain ware would be desirable but we are interested in anything available at all. If interests warrant, I will be happy to post a summary of replies to the board. Thanks in advance, Steve Thompson the various replies follow------------------------ ********************General Interest******************* From: NWHETT@NCSUMVS.BITNET Just wanted to let you know that I am interested in the replies you receive, and if you don't summarize and repost the responses, to request that you forward them to me (nwhett@ncsumvs.bitnet or nwhett@ncsumvs.ncsu.edu). There is a package of programs (DOS- based) available from a fellow named Jurg Ott at Columbia that performs some linkage analysis functions. I don't know if it does mappping in the sense of deriving most likely gene order from three-point crosses, but it is free and might be worth your time to look into. I don't have the address off the top of my head, but if you need it, let me know and I can look it up. Good luck! Ross Whetten ******************************************************************************** From: "Daniel E. Weeks" You may want to try the LINKAGE package. The DOS version is available from: Dr. Jurg Ott Columbia University Box 58 722 West 168th Street New York, NY 10032 E-mail: ott@nyspi.bitnet There is also a VAX/VMS or Unix version available from Dr. Mark Lathrop at the Centre d'Etude Polymorphisme Humain in Paris. Please let me know if you need the address. The LINKAGE package is freely-distributed and is widely used for constructing linkage maps in humans. There is also a version designed specifically for experimental crosses. An alternate package is also available, called the Programs for Pedigree Analysis. This package of programs is available from: Dr. Kenneth Lange Department of Biomathematics University of California Los Angeles School of Medicine Los Angeles, CA 90024-1766 This package is written in FORTRAN and is very easy to port to almost any machine with a good FORTRAN compiler. The MENDEL portion of this package has been used to construct linkage maps in humans (See the most recent issue of the American Journal of Human Genetics). Sincerely, Daniel E. Weeks Department of Human Genetics University of Pittsburgh ******************************************************************************** ********************Linkage Information******************** From: Robert Cottingham There is a very good alternative if you are familiar with linkage analysis, computers and programming. It is the LINKAGE package by Lathrop et al. It is available for DOS, VMS and Unix systems. I would recommend against using it under DOS for anything but small problems. To pick up a copy do an anonymous FTP to corona.med.utah.edu (128.110.231.1) and cd pub/linkage/vms and take it from there. ------------------------------------------------------------ Bob Cottingham Phone: 713/798-4275 Cell Biology, M301 Fax: 790-1275 Baylor College of Medicine Email: bwc@bcm.tmc.edu Houston, TX 77030 ------------------------------------------------------------ ******************************************************************************** From: Jurg Ott Attached is a list of programs available from us for genetic linkage analysis. The LINKAGE program set is probably suitable for the analysis of those sheep families. These programs are what most people in human linkage analysis use nowadays. I currently distribute only the PC version. COMPUTER PROGRAMS USEFUL IN LINKAGE ANALYSIS These programs are designed for IBM type microcomputers, unless indicated otherwise. On disks 5a-5c, below, you will find the current PC version (5.10) of the LINKAGE programs for general and 3-generation pedigrees. Versions prior to 5.1 are no longer supported by us. A version for OS/2 is also available (disk 4). The HOMOG and Linkage Utility programs are now written in standard Pascal and compiled with with Prospero Pascal. Execut able code is available for DOS and OS/2. ORDERING INSTRUCTIONS - PLEASE FOLLOW CAREFULLY 1. Below, sets of files are arranged as numbered disks. Most of these 'disks' hold up to 360 KB characters, but some (identified with 'DD') contain up to 720 KB, and some ('HD') contain up to 1.4 MB. To order programs, send this pamphlet, with the desired items circled (we will return a new pamphlet). Enclose the appropriate number of formatted disks to hold the programs desired, either IBM PC 5-1/4" 360 KB, or high-density 5- 1/4", or 3-1/2" disks (DD or HD) that we will then return (high-density disks hold several of the items listed below). Notice that 360 KB disks will be written on a high-density drive so that they may not be readable on a low-density drive. For 3-1/2" disks, do NOT format a disk labelled DD as a high-density disk. ONLY FORMATTED DISKS WILL BE PROCESSED 2. Enclose one extra empty disk to help cover postage. 3. Enclose an address label (possibly self-sticking) with your address on it. Regular orders---Disks are sent out approximately once a week. No cost. Rush orders---Disks will be mailed on the day the order is received. Handling charges (rush orders only): $100 for postal mail, or Express service charged to your account. $120 when sent by Federal Express charged to our account. Forms of payment: (1) Check made out to Columbia University, enclosed with your order; or (2) Letter stating that you will pay an invoice sent with the disks (government purchase order ok). Katherine Montague/Jurg OTT Tel. (212) 960-2507 Columbia University, Box 58 722 West 168th Street FAX (212) 568-2750 New York, N.Y. 10032 LIST OF AVAILABLE PROGRAMS (see next page) TPS= Turbo Pascal (TP) source code (compiler needed). TPC= Turbo Pascal, compiled for IBM PC FSC= Fortran (Microsoft v.4.01), source and compiled. EXE= executable code Item Contents ---------------------------------------------------------------- LINKAGE programs version 5.10, disk 4 (Prospero Pascal, DOS or OS/2) and disks 5a-5c (Turbo Pascal version 5, DOS). The pro- grams are in compressed form and will have to be decompressed using a program supplied on disks 4 and 5a. Printed documenta- tion (version 5.10, May 1991) will be provided. Our benchmark pedigree is on disk 5b (subdirectory BENCH). LINKAGE programs in Prospero Pascal (OS/2 or DOS, compiled for OS/2 only, for use on machines with or without coprocessor): 4 All programs and documentation [1 HD disk] LINKAGE programs in Turbo Pascal (general and CEPH pedigrees; DOS only): For general pedigrees order 5a+b, for 3-generation pedigrees order 5a+c. 5a Management and utility programs 5b Programs for general pedigrees; benchmark data in \DISK5b\ BENCH 5c Programs for three-generation pedigrees OTHER PROGRAMS (Turbo Pascal version 5 except where noted) 6 Linkage Utility programs, source and compiled for OS/2 (see list at the end) [1 DD disk] 7 NOCOM program for analysis of mixture of distributions. In- cludes the COMPMIX and HIST programs. FSC 8 Linkage Utility programs, source and compiled for DOS [1 DD disk] 9 PC-LIPED (two-point linkage analysis, up to 5 alleles per locus), version Oct. 1988. Includes SEXLODS program for approx. separation of male and female recombination frac- tions. FSC 9a LIPED, same as disk 9 except that up to 6 alleles per locus are allowed and program requires more memory to run. 10 PC-WRITE version 3.02 text editor for data entry (Quicksoft, Inc.) [3 disks, 10a-10c] 14 Programs for homogeneity tests, source and compiled for OS/2 with coprocessor [1 DD disk] 15 same as #14 but compiled for DOS, no coprocessor required [1 DD disk] 16 same as #14 but compiled for DOS, coprocessor required [1 DD disk] 17 Kermit V2.30 program for electronic communication. 18 LIPEDMAX program version Nov. 1987 for iterative estimation of age of onset parameters (lognormal distribution of age at onset). FSC 20a SLINK simulation program, DOS and OS/2 version, Prospero Pascal source code, documentation, and examples [1 DD disk] 20b SLINK compiled for DOS with coprocessor [1 DD disk] 20c SLINK compiled for DOS not requiring coprocessor [1 DD disk] 20d SLINK compiled for OS/2, requiring coprocessor [1 DD disk] 20e SIMULATE program for simulation under no linkage (DOS, OS/2, and VAX, source and compiled) [1 DD disk] 21 SLINK simulation program, VAX VMS source code [1 DD disk] 22a LINKAGE programs for 2-locus disease models (TMLINK, TLINKM, TILINK), source and compiled for DOS requiring coprocessor [1 HD disk] 22b same as #22a but for VAX VMS, source [1 DD disk] 22c same as #22a but compiled for OS/2, requiring coprocessor [1 HD disk] --------------------------------------------------------------- We keep a list of people who ordered programs from us and/or who have taken our linkage courses. These individuals regularly receive the LINKAGE NEWSLETTER which is so far being mailed free of charge a few times a year. LITERATURE (for information purposes only) J. Ott: "Analysis of Human Genetic Linkage", revised edi- tion. Johns Hopkins University Press, Baltimore and London, 1991 ($47.50). Japanese translation of original edition by Soft Science, Tokyo, 1987. E.A. Thompson: "Pedigree Analysis in Human Genetics", Johns Hopkins University Press, Baltimore and London, 1986 ($35). K.E. Davies (editor): "Human Genetic Diseases - A Practical Approach". IRL Press, Oxford England and Washington, D.C., 1986 ($25, softbound; $40, hardbound). PROGRAMS CONTAINED ON DISKS 6 and 8 (version no. in paren- theses) 2BY2 (1.0) carries out Fisher's exact test in 2x2 tables (n<5000). ASSOCIATE (2.3), for two loci with codominant alleles, partitions the chi-square for phenotypic association into two components, (1) due to allelic association, (2) other phenotypic association. BINOM (1.63) calculates binomial probabilities and confi- dence intervals (n<5000). CHIPROB (2.2) computes p-values (upper tail probabilities) for the chi-square distribution. CONTING (2.4) calculates chi-square for contingency table data. EQUIV (2.6) calculates equivalent fully informative observa- tions from a lod score curve. HIST (2.3) produces a histogram. MAPFUN (2.31) converts recombination fractions into map distances (6 mapping functions) and vice versa. NORINV (1.31) accurately computes the normal deviate from a given tail probability. NORPROB (3.2) accurately computes the tail probabilities (p- values) associated with a normal deviate, x. PERMUTE (2.3) produces a list of all n!/2 orders of n gene loci. PIC (1.3) computes for given alleles at one locus the PIC value and heterozygosity. RERI (2.2) calculates and combines relative risks from a set of 2x2 tables and carries out homogeneity tests among the tables. VARCO3 (2.41) approximates mean and variance of an MLE of theta from three values of theta and its log likelihoods or lod scores. The likelihood is approximated by a normal density, i.e., the log likelihood is quadratic. VARCO6 (2.21) approximates means, variances and correlation for two jointly estimated variables, x and y, from six points (x,y) and associated likelihood values. ******************************************************************************** ********************MapMaker Information******************** From: csb@jax.org (Carolyn Blake) Organization: The Jackson Laboratory, Bar Harbor, ME 04609 Mapmaker is available for other 'not fancy' systems as well. We have it running under UNIX with no fancy graphics capabilities. You may also wish to contact Dr. Alan Hillyard (alh@morgan.jax.org). He maintains GBase, a linkage map database of the mouse, and is currently working on databases of linkage maps for other species. ******************************************************************************** From: "Gunnell, Mark" We are currently running MapMaker version 1.9 under VMS version 5.4-2, and it does not require anything beyond standard ascii terminals. We obtained the package from: MAPMAKER Dr. Eric Lander Whitehead Institute 9 Cambridge Center Cambridge, MA 02142 mapm%mitwibr@mitvma.mit.edu Cost was less than $20. Let me know if you need additional information. ------------------------------------------------------------------------------- Mark A. Gunnell | Internet: gunnell@ncifcrf.gov Sci. Applications Analyst | Bitnet: gunnell%ncifcrf.gov@cunyvm.bitnet Advanced Scientific Computing Lab.| Phone: (301) 846-5779 PRI/DynCorp | NCI-FCRDC | PO Box B, Bldg 430 | Frederick, MD 21702-1201 USA | ------------------------------------------------------------------------------- ******************************************************************************** ********************GeneTree Information******************** From: wijsman@max.u.washington.edu Subject: GENETREE distribution GeneTree is finally being released for distribution. We have finally gotten a semi-reasonable agreement on a royaly agreement with the company which produced the driver used internally by the program to do the graphics needed to print pedigrees. As a result, GeneTree will be available at cost to non-profit and educational institutions for $125, which covers the cost of the license for the commercial graphics driver, manuals, diskettes, mailing, etc. A description of GeneTree and its history are below. The GeneTree 1.0 package provides a convenient way to draw family tree diagrams suitable for genetics or geneology using an IBM PC or compatible computer. The package consists of the GeneTree program, which draws pedigree diagrams using a command language, and SC, a menu-driven program that facilitates creation of GeneTree commands. GeneTree and SC are made available with program manuals, examples of family tree diagrams, and a GeneTree Quick Reference Guide. GeneTree is written in the C programming language. Note that it is a DRAWING program and does not compute genetic parameters. Technical requirements: an IBM PC or compatible with 512K or more of memory, and a hard disk with at least 500K unused space, and DOS 3.0 or greater. Salient features of the program are: 1) PEDIGREE DISPLAY: Produces standard pedigree display used in human genetics, using standard symbols, with user control over arrangement and display of the pedigree, symbol size, and placement of text and numeric data around pedigree symbols. Over 30 shading patterns, with full or split symbol shading. 2) SPECIAL PEDIGREE CAPABILITIES: Handles within-generation inbreeding loops without the need for "doubling" a person for drawing complex pedigrees, can display multiple marriages and marriages with no offspring, can draw individuals with only one parent in the pedigree (dummy parents are not necessary), and will draw large pedigrees on multiple pages 3) SIMPLE COMMAND LANGUAGE: Draft pedigrees can be drawn using only three commands, and GeneTree will automatically scale diagrams 4) BATCH OR INTERACTIVE MODE: Operates in either batch or interactive mode, flexible and simple input file structure, can be combined with existing database management of data collection software 5) CURRENT LIMITS: Current maximum pedigree size is about 130 individuals. Maximum number of text and/or number fields around any one pedigree symbol is 25, with a maximum of 256 characters. History of GeneTree is as follows. Robert Hodges wrote the program while he was the system manager for the Alzheimer's disease research center at the University of Washington, partly because of dissatisfaction with what was available for investigators who were doing genetic analyses. In particular, there was nothing at the time at low cost or no cost which could easily interface with the kinds of databases collected in the context of genetic analysis, and which could be used in the context of a variety of analyses to draw pedigrees of varying size and complexity during different stages of the analyses. In order to make it possible to print pedigrees on a variety of printers/plotters, Robert decided to use a commercial driver package. This allows pedigrees to be printed on most if not all printers which are compatible with IBM PCs. The side effect of the use of the driver package, however, is that if we distribute the package, we must pay royalties on the driver. This is why it has taken so long to distribute the program; negotiating lower royalties and coming up with a mechanism to collect royalties was not easy! I have found the program to be extremely useful in my work, which requires examining genetic marker data on pedigrees, constructing haplotypes for multi-site data, using sequential sampling to collect pedigrees which have a trait of interest, etc. Most of these uses involve printing out the same pedigree on a frequent basis with different data, and involve regular interaction with a database. I am the official contact person for furthers inquiries and/or to request a copy of the package. Ellen Wijsman wijsman@saam.bioeng.washington.edu or wijsman@max.washington.edu RG-25 University of Washington Seattle, WA 98195 ******************************************************************************** Again, thank you all for the cooperation. We are very grateful and expect that we will experiment with several of the available packages. If further discussion is requested by this board, I will be happy to oblige. Sincerely, Steve Steven M. Thompson Consulant in Molecular Genetics and Sequence Analysis VADMS (Visualization, Analysis & Design in the Molecular Sciences) Laboratory Washington State University, Pullman, WA 99164-1224, USA AT&Tnet: (509) 335-0533 or 335-3179 FAX: (509) 335-0540 BITnet: THOMPSON@WSUVMS1 or STEVET@WSUVM1 INTERnet: THOMPSON@wsuvms1.csc.wsu.edu From bronze!sol.ctr.columbia.edu!usc!wupost!bcm!bwc Mon Jun 1 10:10:21 EST 1992 Article: 84 of bionet.molbio.gene-linkage Path: bronze!sol.ctr.columbia.edu!usc!wupost!bcm!bwc From: bwc@raven.imgen.bcm.tmc.edu (Robert Cottingham) Newsgroups: bionet.molbio.gene-linkage Subject: Re: Complex traits Message-ID: <12164@gazette.bcm.tmc.edu> Date: 1 Jun 1992 14:48:50 GMT References: <9205291440.AA04020@casbah.acns.nwu.edu> Sender: usenet@bcm.tmc.edu Reply-To: bwc@bcm.tmc.edu Distribution: bionet Lines: 22 Nntp-Posting-Host: raven.imgen.bcm.tmc.edu Originator: bwc@raven.imgen.bcm.tmc.edu In article <9205291440.AA04020@casbah.acns.nwu.edu>, jpang@CASBAH.ACNS.NWU.EDU (JingQi Pang) writes: |> Do you know if there is linkage program running on Sun in C language? |> Any information I will apreciate. Thanks. |> |> --- Jing Qi Pang |> jpang@casbah.acns.nwu.edu |> 312/503-2687 The Sun version of the LINKAGE package can be obtained by anonymous ftp from 128.110.231.1 under /pub/linkage/sun. The programs are written in Pascal, but there have been several reports of success converting the programs automatically into C using p2c which is available by anonymous ftp from labrea.stanford.edu. (Perhaps this should become the beginning of a FAQ for this group.) ------------------------------------------------------------ Bob Cottingham Phone: 713/798-4275 Cell Biology, M301 Fax: 798-5386 Baylor College of Medicine Email: bwc@bcm.tmc.edu Houston, TX 77030 ------------------------------------------------------------