Emmanuel Paradis wrote:
> If you are Bayesian, the trees sampled from an MCMC are here for estimation
> including of the branch lengths, so you use them to compute some sort of
> consensus topology as well as its branch lengths. So it makes sense that
> MrBayes can do a consensus tree with bra
Hi again,
Gwennael Bataille already kindly suggested the use of ade4's
variance.phylog or geiger's phy.anova off-list.
I just realized that pic.ortho is returning intraspecific contrasts.
Could I use those for "normal" anova or posthoc tests? As I am
interested in significant pairwise differences
Hi Scott,
The reason for implementing only the consensus on the topology was after
reading the appropriate chapter in "Inferring Phylogenies". So I'm glad
that Joe himself stepped in. I have added this reference in the help
page (it was already cited in my book with respect to this issue).
I
Hi,
I'm new to this list and although I spent some time now searching for
this issue in the list or other sources, hopefully I haven't overlooked
a relevant thread...
I am comparing gene structural features (derived from fully sequenced
plant genomes (limited taxon sampling)).
Based on Emanuel's
