TCS is a Java computer program to estimate gene genealogies including multifurcations and/or reticulations (i.e. networks). The network estimation implemented in TCS is also known as Statistical Parsimony, which is described in Templeton, A. R., K. A. Crandall and C. F. Sing. 1992. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132:619-633. For a review on networks and instraspecific genealogies you may read Posada D and Crandall KA. 2001. Trends in Ecology and Evolution 16 (1): 37-45
