Hi Marco,
chronos uses specific models for the variation in substitution rates
among branches and I'm not sure whether these models apply to your data.
Maybe you can use chronos with model = "clock" if you can assume that
drift is constant throughout your tree.
HTH
Emmanuel
Le 06/07/2016 1
Geiger has congruify functions that can use pathd8 to make a tree
ultrametric (perhaps using an external chronogram to date it). There's
some code in there to use r8s, as well, but it takes some digging.
Best,
Brian
___
Brian O'Meara
Associate Professor
Dept.
Hi to all of you,
I want to calibrated a relationship tree done with Treemix (Pickrell &
Pritchard 2012) done with SNPs frequency. The branch length of the tree
reflect the amount of genetic drift.
The chronos function from the package ape want tree whose branch lengths
are in number of substituti
Hi Francisca,
The scale of the branch lengths of the chronogram should be defined by
the calibration points provided to chronos(). Maybe you used the default
(age = 1 at the root) so that the branch lengths are (logically) all
less than one.
Best,
Emmanuel
Le 06/05/2015 15:40, Francisca Cu
Dear all,
I am trying to make ultrametric trees from a ML tree. The chronos function
runs all right, but the scale of the calibrated tree I get does not reflect
the calibration I used; instead it seems to be still in substitutions per
site. Is it what I should expect?
Thanks in advance,
Francisca
Hi Fabricia,
This error apparently happens when the root age is unknown and must be
estimated with other parameters. A fixed version of the function can be
found on ape's web site:
http://ape-package.ird.fr/
Best,
Emmanuel
Le 09/04/2014 17:28, Fabricia Nascimento a écrit :
Hi,
I am analy
Hi,
I am analyzing lots of trees in which I need it to be ultrametric. I decided to
use the function chronos, but in the middle of my run I got the following error
message which I don't know the meaning:
Error in nlminb(start.para, f, g, control = opt.ctrl, lower = LOW, upper = UP)
:
NA/NaN
