Hi all,
Thank you for your help, I resolve my first problem (tree
convert to matrix) and the second one I think I must to calculate the
gamma-statistics with the ultrametric tree.
Thank you people,
Cheers
Bryan Morales Pallero
Licenciado en Biología
Biólogo
Laboratorio de
Hello all,
I'm working in the evolution of lizards in Chile, and I
will very grateful if you can help me with the next questions:
1. I need to transform the sample of trees generated by bayesian
inference into a matrix whose values are the branch lenght between tips,
Can I do
Hi Bryan,
On Thu, 02 Dec 2010 03:06:39 -0300 Bryan Morales Pallero
feano...@gmail.com wrote:
Hello all,
I'm working in the evolution of lizards in Chile, and
I will very grateful if you can help me with the next questions:
1. I need to transform the sample of trees generated
Folks --
I believe that the distances predicted from the tree are called patristic
distance. They are a quite old concept. I don't have the literature
accessible right now but believe they were first described by JS Farris or by
Jim Rohlf. Searching on Google using that phrase yields more
Hi Liam,
You are right: thanks for correcting me.
Cheers,
Emmanuel
On Thu, 02 Dec 2010 23:18:39 -0500 Liam J. Revell
lrev...@nescent.org wrote:
I would also add that C-vcv.phylo(tree) gives a matrix, C,
containing
the distances from the root to the common ancestor of each pair of
species.
Emmanuel wrote --
2. I understand that the gamma-statistic index of Pybus and Harvey
applies only to ultrametric trees, there is a similar index for
trees that are not ultrametric?
The 'ultrametricity' of the tree gives it a temporal feature (if
done properly, of course), so that
Folks --
Now that I have had a chance to look up the history:
1. Sokal and Rohlf in 1962 (in Taxon) introduced the
cophenetic correlation.
2. They had a distance called the dendrogrammatic
distance which was (for the ultrametric trees they
considered), half of the patristic distance.
3.
Hello all,
I'm working in the evolution of lizards in Chile, and I
will very grateful if you can help me with the next questions:
1. I need to transform the sample of trees generated by bayesian
inference into a matrix whose values are the branch lenght between tips,
Can I do