RAxML Graphical User Interface

[Alexis]

There have been some new developments in the RAxML GUI developed by
Daniele and Ingo at the Senckenberg Research Institute Dept. Botany
and Molecular Evolution which I will re-post here and annotate with
some comments.

Quote:

Dear raxmlGUI user,

We have just uploaded an update at http://sourceforge.net/projects/raxmlgui/.
The new version includes some graphic changes and implements a couple
of new features:

* implemented the new AA models (as in RAxML version 7.2.8)

Comment: some additional AA models had been added.

* compute consensus using the "dropset" function

Comment: The dropset function implements a rogue taxon identification
algorithm as described in:
N.D. Pattengale, A.J. Aberer, K.M. Swenson, A. Stamatakis, B.M.E.
Moret : "Uncovering Hidden Phylogenetic Consensus in Large Datasets".
IEEE/ACM Transactions on Computational Biology and Bioinformatics,
2011.

* reduced memory ML search (RAxML flag '-F')

This just will skip an optimization under the GTR+GAMMA model in the
end, i.e., saves 75% of the memory required for GAMMA-based
computations with 4 discrete rate categories.

* key board shortcuts
* menu option to inspect the command that will be run in RAxML
* renewed html help file
* link from the help menu to raxmlGUI mailing list
* minor bug fixes

For suggestions and bug reports:
daniele....@senckenberg.de
ingo.m...@senckenberg.de

Best regards
Daniele

[Ingo Michalak]

Dear RAxML user,

We have now uploaded raxmlGUI version 1.0 at http://sourceforge.net/projects/raxmlgui/ with the following new features:

* marginal ancestral state reconstruction (as in RAxML version 7.3.0, see this thread)
* run bootstrap analysis and compute a consensus tree
* enter a user-defined number of bootstrap replicates
* save branch lengths in the bootstrap trees (RAxML flag '-k')
* convert RAxML consensus trees to be compatible with the program FigTree
* export raxmlGUI citation (txt, EndNote, RIS, bib)
* updated html/pdf manual

The main functions of the program are described in our application note:

Silvestro, D. & Michalak, I. (2011) raxmlGUI: A graphical front-end for
RAxML. Organisms Diversity & Evolution, DOI: 10.1007/s13127-011-0056-0

Suggestions and bug reports are much appreciated (contact: raxmlgui[dot]help[at]gmail[dot]com).

Best regards

Ingo

[Ingo Michalak]

Dear all,

we uploaded raxmlGUI version 1.1 on sourceforge (http://sourceforge.net/projects/raxmlgui/).

Here are some of the new features included in the update:
* fast tree search with optional branch lengths and SH values calculation (see this thread: https://groups.google.com/d/topic/raxml/Zd_bqSfz3FE/discussion)
* import/export Nexus alignments using the Dendropy library (with step by step installation process from within raxmlGUI)
* plotting SH values on ML trees
* option to combine all ML trees into a single file (e.g. for consensus tree generation)
* enforce monophyletic topological constraints (see this thread: https://groups.google.com/d/topic/raxml/PmfntMj_NlA/discussion)
* new RAxML executables

As always, feedback is very welcome (raxmlg...@gmail.com)!

Best regards

Ingo

[Ingo Michalak]

Dear RAxML users,

we just made available raxmlGUI 1.2 with the following news

* Includes the newest RAxML executables (v7.3.2, compiled from git hub on July, 31st) for Windows and Mac OSX 

* New Analysis: Compute pairwise distances of taxa, based on a given tree or a MP-starting tree (Only for GAMMA-based models)

* New Amino Acid substitution model GTR_UNLINKED (in which the parameters will be unlinked among partitions)

* Now it is possible to load alignments containing completely undetermined sequences. This is especially helpful for combining data sets.

* After the rogue taxa identification ("DROPSET") a consensus tree will be computed in a pipeline

* Now you can choose models without rate heterogeneity (RAxML flag -V) 

* Minor bug fixes

You find the release on the project's sourceforge page 

https://sourceforge.net/projects/raxmlgui/

Comments and suggestions are highly appreciated (raxmlg...@gmail.com)!

Best regards

Ingo

[Felipe G Grazziotin]

Dear RAxML users,

I'm trying to figure out how to set up a negative constraint (converse constraint) in RAxML.
I'd like to infer the best tree in which the constraint group is not present. Does anyone have a clue on how to do such constraint?

Many thanks for any help.

Felipe

[Alexandros Stamatakis]

Hi Felipe,

This option is not available in RAxML, i.e., you can't specify negative
constraints.

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

[Ingo Michalak]

Dear RAxML user,

we uploaded a small update of raxmlGUI, mainly to fix a bug, introduced in the previous version, that prevented the concatenation of alignments. 

In addition we updated the RAxML executable (to 7.4.2), now with support for FASTA input files.

Please find the update on http://sourceforge.net/projects/raxmlgui/

Questions and other feedback are very welcome: raxmlG...@gmail.com!

Best,

Ingo

[Julieta]

Hello, 

I´m trying to build a phylogenetic tree based on the 16s rRNA sequences of several bacteria belonging to the same genera. For this porpose I would like to use the RAxML Graphical User Interface. Is there any tutorial where I can find the way of selecting the best alignment tool, the criteria used for cutting the sequences after their alignment, it convertion to the phylip format, the selection of the best model for performing ML and the parameters to be used?. I´m quite new in this area and I only want to build a 16s phylogenetic tree of less than 30 organism and obtain a reliable tree.

Thank you in advance.

Juli

[Alexandros Stamatakis]

Dear Juli,

I'd suggest you should read a standard text book on phylogenetics or
search the web a bit for such tutorials. We don't offer something like this.

Alexis

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[Ashutosh Singh]

hello guys

  I am trying to do partitioned ML analysis using raxmlGUI. I have combined two sequence data set (nucleotide sequence) as one and used the option "Set/Edit partitions". I need to set two different models to the partitions.How to do that?? or its better to load individual allignment file of the two sequence data set??

please help

Ashu

[Alexandros Stamatakis]

dear ashu,

please keep in mind that the RAxML GUI is not developed by me and my
lab, hence we don't provide direct support for the GUI via this group.

however the GUI developers are on here as well and might answer.

alexis

On 20.05.2015 10:25, Ashutosh Singh wrote:
> hello guys
> I am trying to do partitioned ML analysis using raxmlGUI. I have
> combined two sequence data set (nucleotide sequence) as one and used the
> option "Set/Edit partitions". I need to set two different models to the
> partitions.How to do that?? or its better to load individual allignment
> file of the two sequence data set??
>
> please help
>
> Ashu
>
> On Tuesday, July 19, 2011 at 12:31:34 AM UTC+5:30, Alexis wrote:
>
> There have been some new developments in the RAxML GUI developed by
> Daniele and Ingo at the Senckenberg Research Institute Dept. Botany
> and Molecular Evolution which I will re-post here and annotate with
> some comments.
>
> Quote:
>
> Dear raxmlGUI user,
>
> We have just uploaded an update at
> http://sourceforge.net/projects/raxmlgui/

> <http://sourceforge.net/projects/raxmlgui/>.

> The new version includes some graphic changes and implements a couple
> of new features:
>
> * implemented the new AA models (as in RAxML version 7.2.8)
>
> Comment: some additional AA models had been added.
>
> * compute consensus using the "dropset" function
>
> Comment: The dropset function implements a rogue taxon identification
> algorithm as described in:
> N.D. Pattengale, A.J. Aberer, K.M. Swenson, A. Stamatakis, B.M.E.
> Moret : "Uncovering Hidden Phylogenetic Consensus in Large Datasets".
> IEEE/ACM Transactions on Computational Biology and Bioinformatics,
> 2011.
>
> * reduced memory ML search (RAxML flag '-F')
>
> This just will skip an optimization under the GTR+GAMMA model in the
> end, i.e., saves 75% of the memory required for GAMMA-based
> computations with 4 discrete rate categories.
>
> * key board shortcuts
> * menu option to inspect the command that will be run in RAxML
> * renewed html help file
> * link from the help menu to raxmlGUI mailing list
> * minor bug fixes
>
> For suggestions and bug reports:

> daniele....@senckenberg.de <javascript:>
> ingo.m...@senckenberg.de <javascript:>
>
> Best regards
> Daniele

[Ingo Michalak]

Dear Ashu,

RAxML does not allow for different models with DNA data sets. For the reasoning why this is the case, please read the RAxML8.x manual. For questions regarding raxmlGUI, please contact us directly on raxmlg...@gmail.com .

cheers

Ingo