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
>
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>
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