is raxml output best ML tree an unrooted tree?

[Niu Yulong]

Hi:

I am using the RAxML-HPC BlackBox to infer the phylogenetic tree. After it is done, I got two tree files "RAxML_bestTree.result" and "RAxML_bipartitions.result". From the RAxML manual, the output best tree is a maximum likelihood tree which is unrooted. The bipartitions tree should be the same as best tree, but with the bootstrap number. However, when I test these two tree by a third part software (R language with "ape" package), the results are wired. The best tree is tested as a rooted tree. 

So I would like to ask the type (rooted or unrooted) of the two output trees. 

The following is the code and results by R:

> besttree <- read.tree('RAxML_bestTree.result')

# is.rooted() is a function provided by "ape" package to test

# whether the tree is rooted (return TRUE) or not (return FALSE)

> is.rooted(besttree)

[1] TRUE

> biparttree <- read.tree('RAxML_bipartitions.result')

> is.rooted(biparttree)

[1] FALSE

Thanks,

Yulong

[Alexandros Stamatakis]

did you specify an outgroup for the tree inference?

alexis

--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[Niu Yulong]

Hi Alexis:

Thank you so much for your reply. I checked the toolkit in CIPRES, and I left the "Outgroup (one or more comma-separated outgroups, see comment for syntax)"  as the default value which is blank. So, I think I did not specify any outgroups. Could you please give some suggestions?

Thanks,

Yulong

在 2014年10月4日星期六UTC-4上午5时14分03秒，Alexis写道：

[Alexandros Stamatakis]

well in that case all output trees should be unrooted, can you send me
the two trees please such that I can have a look?

alexis

On 10/04/2014 10:47 PM, Niu Yulong wrote:
> Hi Alexis:

[Niu Yulong]

Hi Alexis:

Yeah, sure. I upload the output files from RAxML-HPC BlackBox to dropbox with the download link 

https://www.dropbox.com/s/7d1h3mjew296ow6/Cipres_Data.tar.gz?dl=0

If you cannot get the file, please inform me. 

Thanks,

Yulong

在 2014年10月5日星期日UTC-4上午1时53分18秒，Alexis写道：

[Alexandros Stamatakis]

Hi Yulong,

Just checked the code, the newick tree files and also using Dendroscope,
the tree in the bipartition tree file is unrooted, could it be a bug in
the tool you are using?

I'd assume that maybe the script gets confused by the node lables that
form part of the bipartition file.

Cheers,

Alexis

[Niu Yulong]

Hi Alexis:

Really thanks for your help and the test work. So it means both of the output trees ("RAxML_bestTree.result" and  "RAxML_bipartitions.result") should be unrooted based on my input parameters. For the tree files, RAxML puts a trifurcation at the root to represent an unrooted tree, like (A, B, (C, D)) or (A, (C, D), B).  Am I right?

Thanks,
Yulong

在 2014年10月8日星期三UTC-4上午4时22分04秒，Alexis写道：

[Alexandros Stamatakis]

Hi Yulong,

> Really thanks for your help and the test work. So it means both of the
> output trees ("RAxML_bestTree.result" and "RAxML_bipartitions.result")
> should be unrooted based on my input parameters.

Yes, they are.

> For the tree files, RAxML
> puts a trifurcation at the root to represent an unrooted tree, like (A, B,
> (C, D)) or (A, (C, D), B). Am I right?

Yes, I checked for this visually by looking at the Newick tree files.

Alexis

[Niu Yulong]

Hi Alexis:

Thanks, it helps me a lot.

Yulong

在 2014年10月9日星期四UTC-4上午1时21分43秒，Alexis写道：