TMAP is a set of programs for building genetic maps, similar to CarthaGène, JoinMap, and MapMaker. It includes a program phasing which will determine the phase information from phase-unknown outbred pedigrees. It uses a HMM maximum likelihood model which accounts for errors in the genotyping data. This has greatly reduced the tendency of dense maps to have exaggerated sizes. TMAP accepts marker data in the CartaGène format, but also supports its own easier-to-use format. There is no support for quantitative trait linkage (QTL) analysis. The programs' functionality is further described in the README and the algorithms are detailed in Cartwright and Cartwright et al.
TMAP has two interfaces: a command line interface and a graphical Java interface. Almost all capabilities are available from either interface. One exception is that it is only possible to group markers into linkage groups using the graphical interface. Also, the command-line version of phasing gives more detailed errors than the graphical version.
The command line binaries can be built by downloading the C source code compiling. They have been confirmed to work on Solaris, Linux, and Mac OS X, but they should compile on any Unix-like system. Building the Java interface requires both the C and Java source code and thus also the Java Development Kit from Sun.
TMAP was written by Dustin Cartwright while employed at Myriad Genetics. It is freely available under a 3-clause BSD-stye license.
The latest version is 1.1:
Older versions are also available:
Presents the likelihood model and other aspects of the genetic map construction.
Presents the phase determination algorithm implemented in the program phasing.
Presents a genetic map in grapevine which was built using TMAP.