Hi Joseph,
i accomplished installing treePL by following the instructions on the treePL
page (https://github.com/blackrim/treePL/wiki/Installation) but had to install
gcc 4.9 and nlopt manually.
gcc 4.7 didn't work.
The rest worked fine with homebrew!
Cheers,
Franz
Joseph W. Brown josep...@umich.edu hat am 31. Dezember 2014 um 17:46
geschrieben:
Franz,
Yes, Mac has changed enough recently that installing the dependencies can be a
horrific hassle (specifically: the default use of clang instead of gcc).
A couple of options:
1. Install dependencies with homebrew http://brew.sh/.
2. Override the default use of clang, and instead use gcc.
3. If all else fails, and it is not too much trouble, use a virtual box, and
install/use treePL in some flavour of linux. This should work flawlessly.
HTH.
JWB.
Joseph W. Brown
Post-doctoral Researcher, Smith Laboratory
University of Michigan
Department of Ecology Evolutionary Biology
Room 2071, Kraus Natural Sciences Building
Ann Arbor MI 48109-1079
josep...@umich.edu
On 31 Dec, 2014, at 11:34, Franz Krah f.k...@mailbox.org wrote:
Thanks a lot Brian!
Took me the whole day but finally treePL works fine although there were some
difficulties with Yosemite and the version of c++.
The tree - reorder(tree) trick didn't do the trick.
Cheers,
Franz
Brian O'Meara omeara.br...@gmail.com hat am 30. Dezember 2014 um 19:56
geschrieben:
The programs r8s, pathd8, and treepl can all take a phylogram and return a
chronogram, but they're not within R (though they could be wrapped). You
could also infer a chronogram from the start using Beast or MrBayes, though
the large size of the tree may make it difficult.
One simple thing to try before all this, though, is pass your tree through
a reorder() function call (using default arguments) before passing it to
chronos: (i.e.,
tree - read.tree(full_Cipres_Data/RAxML_bestTree.tre)
*tree - reorder(tree)
tree - chronos(tree, lambda = 1, model =
correlated, quiet = FALSE,
calibration = makeChronosCalib(tree),
control = chronos.control())
Sometimes the imported tree structure, while valid, can be an issue for
ape and I find doing this reordering can fix weird errors.
Best,
Brian
___
Brian O'Meara
Assistant Professor
Dept. of Ecology Evolutionary Biology
U. of Tennessee, Knoxville
http://www.brianomeara.info
Postdoc collaborators wanted: http://nimbios.org/postdocs/
Calendar: http://www.brianomeara.info/calendars/omeara
On Tue, Dec 30, 2014 at 4:18 AM, Franz Krah f.k...@mailbox.org wrote:
Dear all,
I used chronos to make a large phylogeny (~3600 species) ultrametric.
The tree is rooted and binary.
With the following code I get the error:
tree - read.tree(full_Cipres_Data/RAxML_bestTree.tre)
tree - chronos(tree, lambda = 1, model = correlated, quiet = FALSE,
calibration = makeChronosCalib(tree),
control = chronos.control())
Error:
In nlminb(start.para, f, g, control = opt.ctrl, lower = LOW, upper = UP) :
NA/NaN function evaluation
This error was posted before some times but I didn't find a satisfying
answer.
I tried out some things but didn't helped: altering the root in different
ways,
altering the model, altering lambda. The functions worked fine with
smaller
phylogenies before!
Hope someone found a solution!
Are there other ways of making my tree ultrametric?
Cheers, Franz
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