[Chih-Horng Kuo] Home: Software: genePed

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Description

This program is designed to generate gene genealogies that are either independent of each other or all share one common organismal pedigree. My purpose of writing this program is to test if gene trees that share one common organismal pedigree would have a higher level of genealogical concordance in terms of their topology frequency distribution. Details of the simulation model and main findings are discussed in Kuo and Avise (2008).

The source code is written in C++ and can be compiled by any GNU C++ compiler (e.g., g++). The source code file is self-contained and does not need any other header/function files. The only external functions used are all from the Standard Template Library (STL).

The sample input file is fully annotated. The operation of the program is self-explanatory, only involves entering input/output file names and few settings.

NOTE: This program was written to serve a specific purpose rather than designed as a generic simulator. However, several functions in the program could be reused for building other simulation programs. If you think the program can be modified for using in other studies and would like to discuss the possibility of collaboration, please send me an email.

Input file format (IMPORTANT!)

This program can only read ASCII text files (e.g. MS-DOS text or text-only).

References

Kuo CH, Avise JC. 2008. Does organismal pedigree impact the magnitude of topological congruence among gene trees for unlinked loci? Genetica, 132, 219-225. DOI: 10.1007/s10709-007-9167-0