[Chih-Horng Kuo] Home: Software: phyloBreak



These two programs are designed to simulate gene genealogies (PhyloBreak) and to analyze phylogeographic breaks in these gene genealogies (BreakAna). Both programs are written in C++ and can be compiled by any GNU C++ compiler (e.g., g++). The source code files are self-contained and do not need any other header/function files. The only external functions used are all from the Standard Template Library (STL).

The sample input file for PhyloBreak (sample.dsp.txt) contains all the instructions needed for the program to run, and has detailed annotation for each part of the instruction. Any further questions regarding preparation of the input file can be directed to the author.

The operation is self-explanatory (only involves entering input/output file names), details of the algorithms are discussed in Kuo and Avise (2005).

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!)

These programs can only read ASCII text files (e.g. MS-DOS text or text-only).


Kuo CH, Avise JC. 2005. Phylogeographic breaks in low-dispersal species: the emergence of concordance across gene trees. Genetica, 124, 179-186. DOI: 10.1007/s10709-005-2095-y