Linkage Interface is an application for organizing genetic linkage data in a way that is easily interfaced with Linkage programs. In our early attempts to perform linkage analysis, we found that entering genotype data using a text editor was mind-numbing, error-prone, and in violation of the Geneva convention. The existing linkage programs do not provide organized methods for entry and editing of genotype data. Linkage Interface is an attempt to make genotype entry and editing more user-friendly and less prone to typing errors. This program is designed as an organizational bridge between the raw polymorphic data and the Linkage programs. The current version of Linkage Interface (version 3.1) outputs files in the format used by the LINKAGE set of programs. This program is NOT a replacement for the Linkage programs. However, it does make their use more efficient and less prone to human error. This program has recently been described in CABIOS 9: 757-9, 1993.
Linkage Interface was developed using Hypercard version 2.2. Any computer that has system 7.0 or greater can run this program. However, Hypercard is NOT needed to use Linkage Interface - the program is a stand-alone application. In addition to the application program, there are three additional stacks bundled with the package. One is a directory stack that serves as a "home" equivalent. Any genotype data file can be accessed from this stack (i.e. it might be useful to make an alias or stick the original in the apple menu folder). The second stack is a help stack for using Linkage Interface. The final stack is the Linkage Interface Stack, into which genotype data is stored. As explained more fully in the help stack, this original Linkage Interface Stack should not be altered. Use the directory stack each time you wish to enter a new family (see the help stack for more details). If you wish to update Linkage Interface stacks which were created with versions previous to 3.0, you must obtain specific update instructions from me (address below). Sorry about this inconvenience, but making Linkage Interface a stand-alone application will make all versions following 3.0 much easier to update.
Notice that after expanding the self-extracting archive, there is one application folder and this teachText document. Place the folder (which contains the four files) into your applications folder (or a similar location). Open the application folder and double click on the help stack. It should tell you all you want to know about Linkage Interface.
Linkage Interface is FREEWARE. BonBini software retains all copyrights of this program. Use of this program, in part or whole, for commercial reasons is punishable by death (unless we approve it first). If you use the program, all I ask is that you drop me a note to tell me if you like or hate it. Include any constructive criticism you might have. If you think you would use the program if it could be changed or customized slightly, let me know. For example, if enough people are interested in a different output file format, I'll add it to the next version. If you're nice I'll change it to your liking. If you're not nice but it seems like a reasonable suggestion, I'll still probably change it. If you want to change it yourself, go for it. Just don't distribute a modified copy. If you register your copy (i.e. tell me about it if you didn't get it from me), you will be among the first to receive the upgrades! I hope you find this program as useful as we do. As mentioned in the help, I am planning an upgrade which will include clinical database stacks sometime in the future. For those of you who do X-linked stuff, the genotype error analysis currently assumes autosomal inheritance, so for the time being you'll have to ignore some of the reported "errors".
