Hi George, Nice comparison! It would be interesting to see if the difference between ape and rncl is always in the same direction. It seems that the trees in your test are all relatively small (timings are concentrated around 1 ms). Apparently, read.tree scales a bit better than
Hi Klaus, Since I'm actually working with the complete PANTHER 11.1 database, I wrote a short document in our project's website comparing both ape and rncl reading ~13,000 trees. ape::read.tree does the job and identifies and reads the singleton as expected. Overall, while I see that the new
Dear George & list, you can try install the development version of ape, which can handle singleton nodes: download.packages("ape", ".", repos = "http://ape-package.ird.fr/;) and than install the package from source. See http://ape-package.ird.fr/ape_installation.html for more details. For you tree
Hi George. Mario is correct that phytools can read a tree with singleton nodes (if that is indeed your problem), but the name of the function is read.newick. Good luck! - Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston web:
Hi Mario, That sounds great! Thanks, George G. Vega Yon +1 (626) 381 8171 http://cana.usc.edu/vegayon On Tue, Sep 5, 2017 at 2:08 PM, Mario José Marques-Azevedo < mariojm...@gmail.com> wrote: > Hi, George, > > Ape package do not read tree with singletons, yet. New version will read. > You can
Hi, George, Ape package do not read tree with singletons, yet. New version will read. You can use readTree from phytools package for while. Best regards, Mario On 5 Sep 2017 5:53 p.m., "George Vega Yon"
wrote: Hi, When trying to read this tree with the ape::read.tree