Chromtree: maximum likelihood estimation of chromosomal phylogenies. We wish to examine the phenomenon of chromosomal evolution using the theory of maximum likelihood, such has been done previously for DNA and amino acid sequence evolution. We introduce a computer package, CHROMTREE, which is an early step in developing a maximum likelihood framework for the evolution of chromosomes. CHROMTREE implements new stochastic models for the evolution of linear chromosomes together with maximum likelihood and pairwise tree-building methods, for both the one chromosome and the many chromosome cases. The steps and problems involved in a chromosomal phylogenetic analysis will be described by considering the case of a single linear chromosome. Future work that must be carried out in order to validate the use of such a framework will be outlined.
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