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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