m.moeller at rbge.org.uk wrote:
> I am looking for methods or software (preferably pc or mac) to
> simultaneously analyse three phylogenetic trees (I have three
> alignment matrices of the same set of taxa based on three different
> genes).
> Does anyone know how to do this?
> Thanks
> Michael
>m.moeller at rbge.org.uk
There is an extensive literature on the appropriate means of
phylogenetically analyzing more than one dataset. Much of this debate
has been going on in the pages of Systematic Biology and Taxon to name
but two journals. In essence the debate centers on whether one should
combine data (the "total evidence" approach) to estimate a single tree
or whether one should combine the trees estimated separately from each
dataset (the "congruence" approach). With both of these approaches,
there are diagnostic statistical/randomization procedures that have been
designed to test whether two or more datasets contain the same type of
phylogenetic information and can, in fact, be combined. If they don't,
then attempting to estimate a single phylogeny for all genes may be
inappropriate.
As a starting point, it is probably worthwhile looking at issues of
Systematic Biology over the last couple of years. There are papers that
do what you are trying to do, with pretty good bibliographies.
Allen Rodrigo
