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 version of the read.tree function is significantly faster, it does not seem to be significantly faster than rncl (both perform pretty good).
You can find the document here: https://github.com/USCbiostats/aphylo/blob/master/playground/ape_now_supports_singletons.md Best, George G. Vega Yon +1 (626) 381 8171 http://cana.usc.edu/vegayon On Tue, Sep 5, 2017 at 5:55 PM, Klaus Schliep <klaus.schl...@gmail.com> wrote: > 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 the new version seems to import tree fine. > Emmanuel and I are keen to get feedback on the new read.tree() function so > please give it a try. > Kind regards, > Klaus > > > > > On Tue, Sep 5, 2017 at 5:37 PM, Liam J. Revell <liam.rev...@umb.edu> > wrote: > >> 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: http://faculty.umb.edu/liam.revell/ >> email: liam.rev...@umb.edu >> blog: http://blog.phytools.org >> >> >> On 9/5/2017 4:17 PM, George Vega Yon wrote: >> >>> 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 use readTree from phytools package for while. >>>> >>>> Best regards, >>>> >>>> Mario >>>> >>>> >>>> On 5 Sep 2017 5:53 p.m., "George Vega Yon" <g.vega...@gmail.com> wrote: >>>> >>>> Hi, >>>> >>>> When trying to read this tree with the ape::read.tree function : >>>> >>>> ((((((((((((((AN14:0.000,AN15:0.000):0.000[&&NHX:Ev=0>1:S= >>>> Homo-Pan:ID=AN13],(AN17:0.000,AN18:0.000):0.000[&&NHX:Ev=0> >>>> 1:S=Murinae:ID=AN16]):0.000[&&NHX:Ev=0>1:S=Euarchontoglires: >>>> ID=AN12],(AN20:0.000,AN21:0.000):0.000[&&NHX:Ev=0>1:S= >>>> Laurasiatheria:ID=AN19]):0.000[&&NHX:Ev=0>1:S=Eutheria: >>>> ID=AN11],AN22:0.004):0.003[&&NHX:Ev=0>1:S=Mammalia:ID=AN10] >>>> ,AN23:0.000):0.014[&&NHX:Ev=0>1:S=Amniota:ID=AN9],AN24:0. >>>> 017):0.021[&&NHX:Ev=0>1:S=Tetrapoda:ID=AN8],((AN27:0. >>>> 066,AN28:0.052):0.010[&&NHX:Ev=1>0:ID=AN26],(AN30:0.031, >>>> AN31:0.014):0.003[&&NHX:Ev=1>0:ID=AN29]):0.021[&&NHX:Ev=0> >>>> 1:S=Teleostei:ID=AN25]):0.147[&&NHX:Ev=0>1:S=Osteichthyes: >>>> ID=AN7],AN32:0.194):0.104[&&NHX:Ev=0>1:S=Deuterostomia:ID= >>>> AN6],((AN35:0.020,AN36:0.038):0.416[&&NHX:Ev=0>1:S= >>>> Caenorhabditis:ID=AN34],((AN39:0.119,AN40:0.131):0.154[& >>>> &NHX:Ev=0>1:S=Insecta:ID=AN38],AN41:0.317):0.104[&&NHX:Ev=0> >>>> 1:S=Arthropoda:ID=AN37]):0.118[&&NHX:Ev=0>1:S=Ecdysozoa: >>>> ID=AN33],AN42:0.381):0.594[&&NHX:Ev=0>1:S=Bilateria:ID=AN5] >>>> ,AN43:2.000):0.414[&&NHX:Ev=0>1 >>>> :S=Eumetazoa:ID=AN4],((((((((AN52:0.484,AN53:0.427):0.418[& >>>> &NHX:Ev=0>1:S= >>>> Saccharomycetaceae:ID=AN51],AN54:0.733):0.320[&&NHX:Ev=0> >>>> 1:S=Saccharomycetaceae-Candida:ID=AN50],AN55:0.808):0.290[&& >>>> NHX:Ev=0>1:S= >>>> Saccharomycetales:ID=AN49],(AN57:0.793,((AN60:0.206,AN61: >>>> 0.186):0.143[&&NHX:Ev=0>1:S=Sordariomyceta:ID=AN59],AN62: >>>> 0.331):0.332[&&NHX:Ev=0>1:S=Sordariomycetes-Leotiomycetes: >>>> ID=AN58]):0.467[&&NHX:Ev=0>1:S=Pezizomycotina:ID=AN56]):0. >>>> 432[&&NHX:Ev=0>1:S=Pezizomycotina-Saccharomycotina:ID=AN48], >>>> AN63:0.864):0.223[&&NHX:Ev=0>1:S=Ascomycota:ID=AN47],(AN65: >>>> 0.613,AN66:0.930,AN67:0.755):0.332[&&NHX:Ev=0>1:S= >>>> Basidiomycota:ID=AN64]):0.618[&&NHX:Ev=0>1:S=Dikarya:ID= >>>> AN46],((((((AN74:0.337,AN75:0.406):0.298[&&NHX:Ev=0>1:S= >>>> Saccharomycetaceae:ID=AN73],AN76:0.578):0.338[&&NHX:Ev=0> >>>> 1:S=Saccharomycetaceae-Candida:ID=AN72],AN77:0.567):0.304[&& >>>> NHX:Ev=0>1:S= >>>> Saccharomycetales:ID=AN71],(AN79:0.379,((AN82:0.398,AN83: >>>> 0.403):0.191[&&NHX:Ev=0>1:S=Sordariomyceta:ID=AN81],AN84: >>>> 0.366):0.140[&&NHX:Ev=0>1:S=Sordariomyc >>>> etes-Leotiomycetes:ID=AN80]):0.457[&&NHX:Ev=0>1:S= >>>> Pezizomycotina:ID=AN78]):0.331[&&NHX:Ev=0>1:S=Pezizomycotina- >>>> Saccharomycotina:ID=AN70],AN85:0.737):0.128[&&NHX:Ev=0> >>>> 1:S=Ascomycota:ID=AN69],(AN87:0.599,AN88:0.698):0.161[&&NHX: >>>> Ev=0>1:S=Basidiomycota:ID=AN86]):0.398[&&NHX:Ev=0>1:S= >>>> Dikarya:ID=AN68]):0.117[&&NHX:Ev=1>0:ID=AN45],(AN90:0.984, >>>> AN91:0.893):0.158[&&NHX:Ev=1>0:ID=AN89]):0.262[&&NHX:Ev=0> >>>> 1:S=Fungi:ID=AN44]):0.394[&&NHX:Ev=0>1:S=Opisthokonts:ID= >>>> AN3],(AN93:0.457,AN94:0.462):0.860[&&NHX:Ev=0>1:S= >>>> Dictyostelium:ID=AN92]):0.301[&&NHX:Ev=0>1:S=Unikonts:ID= >>>> AN2],AN95:1.440,AN96:2.000):2.000[&&NHX:Ev=0>1:S=Eukaryota: >>>> ID=AN1])[&&NHX:Ev=1>0:ID=AN0]; >>>> >>>> I get the following error: "The tree has apparently singleton node(s): >>>> cannot read tree file. Reading Newick file aborted at tree no. 1", >>>> which seems to be wrong since I can actually read this tree without >>>> problem >>>> using rncl::read_newick_phylo and this online tool >>>> http://etetoolkit.org/treeview/?treeid=6e192f20a3226cfdde219531cc533e >>>> 9f&algid=ce443ed1e53858bf4e11d1e069c7a927 >>>> >>>> I understand that this particular tree is a modified version of Newick's >>>> format, but this is the first time that I have problems reading this >>>> type >>>> of tree. >>>> >>>> Here my session info: >>>> >>>> devtools::session_info() >>>>> >>>> Session info >>>> ------------------------------------------------------------ >>>> ----------------------------------------------------------------- >>>> setting value >>>> version R version 3.4.1 (2017-06-30) >>>> system x86_64, linux-gnu >>>> ui RStudio (1.0.143) >>>> language (EN) >>>> collate en_US.UTF-8 >>>> tz America/New_York >>>> date 2017-09-05 >>>> >>>> Packages >>>> ------------------------------------------------------------ >>>> --------------------------------------------------------------------- >>>> package * version date source >>>> ape 4.1 2017-02-14 CRAN (R 3.4.0) >>>> assertthat 0.2.0 2017-04-11 CRAN (R 3.4.0) >>>> base * 3.4.1 2017-06-30 local >>>> compiler 3.4.1 2017-06-30 local >>>> datasets * 3.4.1 2017-06-30 local >>>> devtools 1.13.3 2017-08-02 CRAN (R 3.4.0) >>>> digest 0.6.12 2017-01-27 CRAN (R 3.4.0) >>>> graphics * 3.4.1 2017-06-30 local >>>> grDevices * 3.4.1 2017-06-30 local >>>> grid 3.4.1 2017-06-30 local >>>> lattice 0.20-35 2017-03-25 CRAN (R 3.4.1) >>>> magrittr 1.5 2014-11-22 CRAN (R 3.4.0) >>>> memoise 1.1.0 2017-04-21 CRAN (R 3.4.0) >>>> methods * 3.4.1 2017-06-30 local >>>> nlme 3.1-131 2017-02-06 CRAN (R 3.4.1) >>>> parallel 3.4.1 2017-06-30 local >>>> prettyunits 1.0.2 2015-07-13 CRAN (R 3.4.1) >>>> progress 1.1.2 2016-12-14 CRAN (R 3.4.1) >>>> R6 2.2.2 2017-06-17 CRAN (R 3.4.0) >>>> Rcpp 0.12.12 2017-07-15 CRAN (R 3.4.0) >>>> rncl 0.8.2 2016-12-16 CRAN (R 3.4.1) >>>> stats * 3.4.1 2017-06-30 local >>>> tools 3.4.1 2017-06-30 local >>>> utils * 3.4.1 2017-06-30 local >>>> withr 2.0.0 2017-07-28 CRAN (R 3.4.0) >>>> >>>> >>>> Any ideas? >>>> >>>> Best, >>>> >>>> George G. Vega Yon >>>> +1 (626) 381 8171 >>>> http://cana.usc.edu/vegayon >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> R-sig-phylo mailing list - R-sig-phylo@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >>>> Searchable archive at http://www.mail-archive.com/r- >>>> sig-ph...@r-project.org/ >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> R-sig-phylo mailing list - R-sig-phylo@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >>>> Searchable archive at http://www.mail-archive.com/r- >>>> sig-ph...@r-project.org/ >>>> >>>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> R-sig-phylo mailing list - R-sig-phylo@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >>> Searchable archive at http://www.mail-archive.com/r- >>> sig-ph...@r-project.org/ >>> >>> >> _______________________________________________ >> R-sig-phylo mailing list - R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> Searchable archive at http://www.mail-archive.com/r- >> sig-ph...@r-project.org/ >> > > > > -- > Klaus Schliep > Postdoctoral Fellow > Revell Lab, University of Massachusetts Boston > http://www.phangorn.org/ > > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
