Welcome to MSTMapMSTMap is a software tool that is capable of constructing genetic linkage maps efficiently and accurately. It can handle various mapping populations including BC1, DH, Hap, and RIL, among others. The tool builds the genetic linkage map by first constructing a Minimum Spanning Tree (MST), and hence the name MSTMap. The algorithm implemented in MSTMap is very efficient and can handle ultra-dense maps of up to 10,000~100,000 markers. According to our experimental studies, when the data quality is high, the accuracies of the maps produced by our tool are as good as those by the best tools available in the literature. However, when the data are noisy, the maps generated by our algorithm are significantly better. View this page in Romanian courtesy of azoft How to use MSTMap
You will need to download the source code and compile it
on a Linux machine. To use MSTMap, you need to specify 2 parameters: input_file and output_file.
The following command line demonstrates the usage of MSTMap: The input file formatEach input file consists of two parts, the header and the body. Please refer to example.txt for an example.
How to interpret the output fileThe output file is self-explanatory and easy to understand. It simply lists the markers in each linkage group. The genetic distances between markers are also available from the output file. Please refer to example_map.txt for an example.DownloadsSample Input is a synthetic data set with 100 mapping lines and 100 markers. The markers are spaced at an average distance of 2cMs. 1% of missing and 1% of error genotype calls are introduced to the data set purposely in order to mimic what's happing in reality. The true order of the markers is m0,m1,m2,...,m99 (or its reverse).CopyrightMSTMap is free for academic use only. For questions about the tool, please contact yonghui@cs.ucr.edu. |