Simulating the evolution of biological sequences with neighbor-dependent substitutions
alfacinha is a source-package of object-oriented Python modules for sequence evolution allowing for neighbor-dependent substitutions. This package is aimed at simulating the evolution of sequences along phylogenetic trees. It provides several modules to (1) store and manipulate evolutionary models, (2) store and evolve a sequence and (3) store and manipulate evolutionary trees.
This package is available for UNIX, LINUX or MacOS X operating systems. It runs on Python version 2.(>=2). When installing, do not forget to update yout $PYTHONPATH environment variable.
alfacinha is a very easy to use tool, for which we provide a tutorial to get you started: http://pbil.univ-lyon1.fr/software/alfacinha/tutorial/index.html
If you have any problems or comments about alfacinha, please contact me.