consense trees on CIPRES

43 views
Skip to first unread message

melisa eliana magallanes

unread,
Jun 13, 2019, 9:29:26 AM6/13/19
to ExaBayes
Hi there, I would like to know if is possible run the consensus tree step on CIPRES. how should I make my configuration file?

Thanks, Melisa.

Alexandros Stamatakis

unread,
Jun 13, 2019, 11:13:46 PM6/13/19
to exab...@googlegroups.com
Hi Melisa,

This is something to ask the colleagues that are operating Cipres, as
this is not directly maintained by us.

I've bcced them.

Alexis
> --
> You received this message because you are subscribed to the Google
> Groups "ExaBayes" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to exabayes+u...@googlegroups.com
> <mailto:exabayes+u...@googlegroups.com>.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/exabayes/6bd4e97f-95c8-4938-bd66-e16a0e8c0499%40googlegroups.com
> <https://groups.google.com/d/msgid/exabayes/6bd4e97f-95c8-4938-bd66-e16a0e8c0499%40googlegroups.com?utm_medium=email&utm_source=footer>.
> For more options, visit https://groups.google.com/d/optout.

--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.exelixis-lab.org

Miller, Mark

unread,
Jun 19, 2019, 1:08:43 PM6/19/19
to exab...@googlegroups.com
Thanks. I need a little more information, as I have not used ExaBayes in a while.
I don’t think we have a consensus tree option, and I assumed it was something specified in the config file?
I didn’t see a specific command line option for this. But if one of you refers me by link to the information about what is required, I can put it in place.

Mark
To unsubscribe from this group and stop receiving emails from it, send an email to exabayes+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/exabayes/67ab65d3-04d7-620d-baf9-3eb89a02e465%40gmail.com.

Alexandros Stamatakis

unread,
Jun 19, 2019, 11:10:21 PM6/19/19
to exab...@googlegroups.com
Dear Mark,

There are some additional binaries that come with ExaBayes that perform
the job, see manual at

https://cme.h-its.org/exelixis/web/software/exabayes/manual/index.html

Section 4.1

for instance:

./consense -f ExaBayes_topologies.myRun.0 -n myCons

./credibleSet -f ExaBayes_topologies.myRun.0 -n cred

./postProcParam -f ExaBayes_parameters.myRun.0 -n params

Alexis

Miller, Mark

unread,
Jun 20, 2019, 12:42:50 PM6/20/19
to exab...@googlegroups.com
Great, thanks Alexis.
Is this different than Consense in the Phylip package?
To view this discussion on the web visit https://groups.google.com/d/msgid/exabayes/f2053d1d-c4ba-d00d-ca95-035809d1e8a6%40gmail.com.

Alexandros Stamatakis

unread,
Jun 20, 2019, 2:43:09 PM6/20/19
to exab...@googlegroups.com
yes, it's a tool we implemented,

alexis

Cássia Bitencourt

unread,
Jul 12, 2019, 10:07:13 PM7/12/19
to ExaBayes
Hi Alexis and Mark, I would like to know if consensus tree step are now able on CIPRES? I need for my data.

Thanks a lot, Cássia.

Miller, Mark

unread,
Jul 15, 2019, 10:53:16 AM7/15/19
to exab...@googlegroups.com

Hi Cassia,

 

This feature is available. Unfortunately the CIPRES service is not working right at the moment.

We are investigating. So sorry for the inconvenience.


Mark

--

You received this message because you are subscribed to the Google Groups "ExaBayes" group.
To unsubscribe from this group and stop receiving emails from it, send an email to exabayes+u...@googlegroups.com.

Cássia Bitencourt

unread,
Jul 15, 2019, 2:47:42 PM7/15/19
to ExaBayes
Hi Mark,

thanks a lot for the support. Is there another way for consense (other tool, like a available on Cipres server) or I should to use the command in config file?

Best,
Cássia


Em segunda-feira, 15 de julho de 2019 11:53:16 UTC-3, Miller, Mark escreveu:

Hi Cassia,

 

This feature is available. Unfortunately the CIPRES service is not working right at the moment.

We are investigating. So sorry for the inconvenience.


Mark

 

From: exab...@googlegroups.com <exab...@googlegroups.com> On Behalf Of Cássia Bitencourt
Sent: Friday, July 12, 2019 7:07 PM
To: ExaBayes <exab...@googlegroups.com>
Subject: [exabayes] Re: consense trees on CIPRES

 

Hi Alexis and Mark, I would like to know if consensus tree step are now able on CIPRES? I need for my data.

 

Thanks a lot, Cássia.

Em quinta-feira, 13 de junho de 2019 10:29:26 UTC-3, melisa eliana magallanes escreveu:

Hi there, I would like to know if is possible run the consensus tree step on CIPRES. how should I make my configuration file?

 

Thanks, Melisa.

--
You received this message because you are subscribed to the Google Groups "ExaBayes" group.

To unsubscribe from this group and stop receiving emails from it, send an email to exab...@googlegroups.com.

Miller, Mark

unread,
Jul 15, 2019, 6:07:10 PM7/15/19
to exab...@googlegroups.com

I put an option on the interface to run consense when the job is complete.

To unsubscribe from this group and stop receiving emails from it, send an email to exabayes+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/exabayes/4358f81a-6595-4078-9b0f-2554aff2d32c%40googlegroups.com.

Miller, Mark

unread,
Jul 16, 2019, 2:15:28 AM7/16/19
to exab...@googlegroups.com

The service has been restored, please let me know if you have any issues using consense in the interface. You will probably be the first person other than me to try it.

 

Mark

 

From: exab...@googlegroups.com <exab...@googlegroups.com> On Behalf Of Cássia Bitencourt

Sent: Monday, July 15, 2019 11:48 AM
To: ExaBayes <exab...@googlegroups.com>

To unsubscribe from this group and stop receiving emails from it, send an email to exabayes+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/exabayes/4358f81a-6595-4078-9b0f-2554aff2d32c%40googlegroups.com.

Reply all
Reply to author
Forward
0 new messages