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Joinmap3.0使用说明 评分

Joinmap,这里有详细的使用说明,不过是全英文的讲解。
Contents Introduction Installati Overvie 2 A genotype data population 2 A pairwise data population M p integra Final remarks 8 How to cite JoinMap 3.0? Acknowledgement Using join mat Controlling the program The join Map project 12 The population node LOD scOre 15 The pairwise data population node 16 The grouping node 16 The group node 16 The pairwise data population group node 18 Map ir ap ntegration The mapping node and the mapping procedure The map node 21 The pairwise data population map node E Xternal maps Tutorial 23 Data files 31 Data file characteristics 32 Acus genotype fil le 33 Pairwise data file 39 Map file Translation file 42 Non-Join Map locus genotype file Default file name extensions 46 Tables, examples and reference 47 List of figures List of table 47 st of examp 48 Refere nces ndex 49 Introduction Introduction oinmap is a computer program for the calculation of genetic linkage maps in experimental populations of diploid species. The present version is a completely revised edition based on version 2.0 Stam Van Ooijen, 1995). It has most functionality of that version, some of the very infrequently used parts were not incorporated, while a lot of functionality was added by creating a new powerful user intertace based on MS-Windows Through this interface, many features are software. A very important enhancement is the way the software takes care of the c controlled in the normal Ms-Windows way, thereby allowing an intuitive use of th data; all the user has to do is provide the file with genotype data while the software deals with all subsequent actions on the data, such as selecting subsets of loci or of individuals. This relieves the user of the many edit actions needed under version 2, 0 and because of that invites the user to a better exploration of his or her data. Another significant improvement is the way the grouping of loci into linkage groups can be studied, allowing a much better visual insight into associations bctwccn loci; also, thc grouping calculations wcrc spcd up vcry significantly. A final, but not the least, enhancement is the incorporation of a map charting component, with which the user can create high quality charts of the calculated maps. Installation JoinMap vetsion 3.0 is a program for the Ms-Windows platform. It was tested lo run under Windows 95, and Windows NT 4.0, and is further expected to run tlawlessly under Windows 98, ME and 2000. It comes with an InstallShield installation program that does most of the work. Start the SETUP.EXE program from the set of installation files, e. g. by double-clicking on it from within windows Explorer or My Computer. Choose the settings that you are prompted for and let SETUP.EXE finish. Aftet this process the license file JoNMAP,LIC will be present in the program directory (typically C: Program Files Join Map). This copy Introduction of the license file allows you to use the software under certain limitations such as a maximum of two linkage groups, no printing or exporting. A purchased vetsion o Join map comes with a separate personal license file, which is also named JOINMAPLIC. By replacing thc installed liccnsc filc in the program directory with your personal license file you will gain iull access to the soltware. part from the length of names(maximum of 20) characters for population, locus and linkage group names) there are no limits built into the software, memory for storing data is allocated dynamically only for the amount needed. So, your project size is limited only by the amount of RAM in your PC, for which a size of 64 MB is recommended for reasonably sized projects Overview Start the program using the Windows Start menu. When the program runs you will see a window that is divided into several main parts: on the top the menu and the tool bar with buttons, on the left side there is the navigation pamel on the right side the contents and results pane, and on the bottom the status bar (Figure 1). Once data are loaded the navigation panel will contain a tree, like in w irdows Explorer, in which each node will represent an item, such as a population, a linkage group or a map. The contents-and-tesults panel will contain a set of tabbed pages(tabsheets, in which contents and results of analyses will be displayed concerning the node selected in the navigation tree. When a node becomes selected its corresponding menu item is activated, e.g. for a population node the Population menu and for a group node the Group menu. The formats of data files used by joinMap are described thoroughly in the Data Files chapTer. Some example data files are present in the DemoNata subdirectory of the program directory A genotype data population In Join Map 3.0 your work is organised into a project. You create a new project or open an exis uing project using the File menu. Once a project is opened, you load data into the project. This can be done with the Load Data option in the file menu With this option you can load several types of data files into the project, among which the. most important one is the lacur genotype file(also called lo file), which conTains the genotype codes for the loci of a single segregating population like an F2. Such a population is sometimes referred to as a genotype data population, in conTrast to a pairwise dlala population which will be addressed later. You can load Introduction Menu and tool bar Tabs :: Navigation panel with navigation tree Contents-and-results panel with tabshe Status bar gure 1. Tser interface more populations into a project, if you like. When the population is loaded successfully a population node will appear in the navigation tree and the contents-and- results panel will contain several tabsheets(Figure 2). The Info tabsheet will display a summary on the data loaded into the project. The Duty tabsheet will show a neatly formatted version of the loaded data file, The Lodi and individuals tabsheets allow exclusion of loci and /or individuals from calculations and actions. The other tabsheets are initially empty; they will be filled with results of corresponding calculations using the genotypes of the currently selected (i. e not excluded)set of loci and individuals. Clicking on the(Re- calculate button on the tool bar will start the calculations, and aftet successful completion thc tabshcct will bc filled with its resulLs. Values of Patameters used in calculations can be modified in the Calculation Options from the Options menu The: I acus gent. fire. tabsheet will display the genotype frequencies for each locus in order to study segregation distortion. The Individual genot. free. tabsheet will show the genotype frequencies for each individual. The Similarity of lodi and Similarity of individuals tabsheets will show the Fractions of identical genotypes(Che calculations include the missing genotypes). The LOD Groupings(text) and LOD Groupings(tree) Labsheels will show the grouping of loci. Both Labsheets ate different views of the same analysis; the text view is more suitable for printing, while the tree view has a more attractive visual appearance allowing user interaction and must be used for creating group nodes in the navigation tree necessary for calculating linkage maps The grouping is based upon the test for independence(translated into a LOD score) and is done at several significance thresholds. Loci determined to be significantly associated at the cutrent LOD threshold with at least One member of a Introduction nM即30如 网回区 回囝图因因? MAdama Smitty afos Slimy of ndwduss I LOD gtupisge gasn LoD grospiron gras) nthtusisI Lotus gent fea I Dadu gent fr potmAn 3.C Mcn,245p20d.10:34 11cansad to: 3o1nmap 3.0 avaluation licence; walia unn17 1-11-20o1. acus genotype file: E: \M cdata\n2cdano loc poputation name population type. tndtvtouats: nrvtrunts 10 igure 2. A population node (im20demo)with its vatious tahsheets group will be in the same group. The tree view will show nodes representing th names that consist of three felds: LOD/nr(s in which LOD represents the LOd threshold under which the group was formed, mr represents the group number at that lod threshold (the largest group gets the smallest number), and sige is the number of loci in the group. When you select a certain node in the LOD Groupings tree(by clicking on it), the loci of that group are displayed in the list on the right-hand side of the tabsheet Once you have decided which groups from the IOD Groupings tree you want to use for calculating the linkage map, you need to select their nodes by right clicking. A node selected this way will become red (ot magenta. for the current node)(igure 3 When you have selected all required groups, you subsequently use the Create Groups Figure 3. The creation of groups for mapping Introduction M30- =Pmlsm B神 Locus Growp LOD G auEisg Nos GnD 2 5917311 140 Groun 3 2129 140n(0 Group 4 13: 14D色D Group 5 t8 9402 140n 625 14 655g{s14M Figure 4. A grouping node with five group nodes for Mapping option from the Population menu. If successful, this action will produce in the navigation tree a grouping node (as a child node of the population node) and for each group a groap node as child nodes of the grouping node)(Figure 4) The grouping node has a single tabsheet showing an overview of the division of loci over the groups. Each group node has several tabsheets. The Data tabsheet will first show a brief instruction how to calculate the pairwise recombination frequencies For the sake of brevity pairwise recombination frequencies are called linkages. After successful calculation of the. linkages the Data tabsheet will show the original genotype data only for the loci in the group. The loci tabsheet shows the loci in the group and allows exclusion of them from futther processing. The Ficed ordere tabsheet is the place where you can specify fixed orders for use in the map calculations of the group. The remaining tabshccts contain information on the linkages, one for the Weak, another for the /rong linkages, a Third for Suspec! linkages and a final for Maximum linkages From a group node a. map can he calculated with the Calculate Map option from the Group menu. The map is calculated based on the selected set of loci. Upon successful completion a mapping node will be produced in the navigation tree(as a child node of the gtoup node) and fot each resulting map a map node(as child nodes of the mapping node). The mapping node has a single tabsheet containing the Session log of the calculations, allowing you Lo sludy the delails of the procedure The mapping procedure is basically a process of building a map by adding loci one by one, starting from the most informative pair ot loci for each added locus the best position is searched and a goodness-of-fit measure is calculated. When the goodness-of fit reduces too sharply (too large a jmp ), or when the locus gives rise to negative distances, the locus is removed again. This is continued until all loci Introduction uM印30d 日区 回囝时图团闻·叫倒? Lc函留L阳 IrMNdual aAiegea-LagIapl Lacus genc tea My chst I Loci I Mp tent I Men chisquare earths I Gerot yme pchshibier Groin 由器M Map 3 GIDP 3 Group 4 IOps Figure 5. The navigation tree after the map calculations for Group 2 have been handled once. This is the end of the so-called first round. Subsequently, all loci previously removed are attempted to be added to the map a second time. This can be successful since the map will contain more lodi than at the first attempt. But it may also be unsuccessful again through too large a jump ot negative distances, so chat a locus will be removed once more. This is the second round. After that all loci previously removed are attempted a final time to be added to the map, now ignoring the requirements of maximum allowed reduction in goodness-of-fit and no negative distances. This results in a final or third round. Of course. when all loci are fitted in the first or second round, there will not be subsequent rounds. The results at the end of each round are represented by a map node (figure 5) A map nodle has several tabsheets, the first three are different representations of the map itself, (1)the Map chart,(2 the map as a list, and ( )the map in plain text, ao MapQTT and MapChart (oin Map's companion software for QTT, analysis and s) each serving its own exporting goal, e.g. for(1) Ms-Powerpoint, (2)MS-Excel, hanced map charting, respectively). The Mean chisquare contribs. tabsheet shows for tabsheet will show (afler clicking on the (Re-ycalculate button) the genotypes wlh each locus the average contribution to the goodness-of-fit. The Genette pmbabilitie. low probability conditional on the map and conditional on the genotypes of the neighbouring loci. The next Lwo tabsheets present these probabilities averaged over individuals and over loci, respectively. The final tabsheet will show the Locus genotype frequencies similar to this tabsheet for the population node, but here the loci are ordered according to the. map

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