SDSE: a software package to simulate the evolution of a pair of DNA sequences

An algorithm to simulate DNA sequence evolution under a general stochastic model, including as particular cases all the previously used schemes of nucleotide substitution, is described. The stimulation is carried out on finite, variable length, DNA sequences through a strict stochastic process, according to the particular substitution rates imposed by each scheme. Five FORTRAN programs, running on an IBM PC and compatibles, carry out all the tasks needed for the simulation. They are menu driven and interfaced to the system through a principal menu. All sequence data files used and generated by the SDSE package conform to the standard GenBank database format, thus allowing the use of any sequence retrieved from this databank, as well as the application of other packages to analyse, manipulate or retrieve stimulated sequences.