Help Information


MergeMap was developed by Yonghui Wu (Ph.D. student, Computer Science), Dr. Timothy J. Close (Professor, Botany and Plant Sciences), and Dr. Stefano Lonardi (Associate Professor, Computer Science), at the University of California, Riverside (UCR). Please forward any inquiry to Yonghui Wu ( The web-server is currently hosted by the Department of Computer Science and Engineering, UCR.

Format of the input maps

The individual genetic linkage map is in the following format:

group lg1
m0      0.000
m8      11.183
m7      11.183
m6      12.183
m94     175.020
m95     179.032
m97     183.083
m98     183.083


group lg2
m100    0.000
m108    11.183
m107    11.183
m106    12.183
m194    175.020
m195    179.032
m197    183.083
m198    183.083

Each individual genetic map may consists of multiple linkage groups (LG). Each LG starts with the line "group group_name", where group_name is the name for that LG, followed by the line ";BEGINOFGROUP", and then the main body of the LG. It ends with the line ";ENDOFGROUP" indicating the end of the LG. The main body of the LG consists of multiple lines, each of which corresponds to one marker. Each line specifies the name of the marker as well as the distance (in cm) from the marker to the first marker in the LG. Please refer to example.txt for an example.

Format of the output files

The LGs from the input genetic maps are first divided into clusters according to their marker compositions. Two LGs belong to the same cluster if they share any markers in common.

For each cluster, three graphs in the .gif format are produced. They are saved as lgx.gif, lgx_consensus.gif, and lgx_linear.gif files respectively, where x is the id of the cluster. The graph highlights the conflicts among the individual maps. It also shows the solution by MergeMap as to which marker occurrences are being deleted. An example along with a detailed explanation is given at the download page. The lgx_consensus.gif shows the simplified consensus DAG while the lgx_linear.gif shows the final linearied consensus map.


Y. Wu, P. Bhat, T. J Close, S. Lonardi, On the Accurate Construction of Consensus Genetic Maps CSB 2008 - Computational Systems Bioinformatics Conference, to appear, Stanford, CA, 2008