Re: [R-sig-phylo] Possible Bug in ape::read.tree
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
read_newick_phylo with bigger trees:
R> write.tree(rtree(5), file = "tr.tre")
R> system.time(a <- read.tree("tr.tre"))
utilisateur système écoulé
0.240 0.004 0.245
R> system.time(b <- read_newick_phylo("tr.tre"))
utilisateur système écoulé
0.380 0.020 0.397
R> identical(a, b)
[1] FALSE
R> all.equal(a, b)
[1] TRUE
Best,
Emmanuel
Le 07/09/2017 à 21:39, George Vega Yon a écrit :
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
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
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" 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-
Saccharomycotin
Re: [R-sig-phylo] Possible Bug in ape::read.tree
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
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
> 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" 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=
Re: [R-sig-phylo] Possible Bug in ape::read.tree
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 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" 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.
Re: [R-sig-phylo] Possible Bug in ape::read.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: 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" 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) assertthat0.2.0 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) digest0.6.12 2017-01-27 CRAN (R
Re: [R-sig-phylo] Possible Bug in ape::read.tree
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" 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) > assertthat0.2.0 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) > digest0.6.12 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 2014-11-2
Re: [R-sig-phylo] Possible Bug in ape::read.tree
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 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) assertthat0.2.0 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) digest0.6.12 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) R62.2.2 2017-06-17 CRAN (R 3.4.0) Rcpp 0.12.12 2017-07-15 CRAN (R 3.4.0) rncl
