Simulation of DNA sequence evolution

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  simulation  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  simulated  sequences.

Oliver JL, Marín A, Medina JR. 1989.
SDSE – a Software Package to Simulate the Evolution of a Pair of DNA-Sequences.
Computer Applications in the Biosciences (now Bioinformatics) 5: 47-50 [PDF]