Is PartitionFinder no longer supported by CIPRES?

[Omar Machado]

Hi everyone,

CIPRES has been an excellent and important tool my work on systematics for the last five years or so. Recently, I tried to find PartitionFinder2 on the XSEDE toolkit, but it is missing. 

Is it no longer supported? I'm also unable to run the software on both Windows and Unix due to various bugs and compatibility issues... 

The page of the tool is still up, though [http://www.phylo.org/index.php/tools/partitionfinder2_xsede.html]. And there is no other way of running it online, it seems.

Best,

Omar M. Entiauspe-Neto

[Mark Miller]

Hi Omar,

Thanks for your inquiry. We did remove partionfinder2 from CIPRES at the request of its author. However, a new version, Partitionfinder3 is available through IQTree.

The new version will not be supported as a standalone tool. Let me know if you have any questions about its use in CIPRES..

Best,

Mark

[Vivek Suranse]

Dear Mark,

I had a small query regarding model selection and partition selection tools. Are jmodeltest2 and partitionfinder2 obsolete? Is there any document/webpage/resource that mentions this?

Thanks in advance.

Sincerely,

Vivek

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Vivek Suranse,

Evolutionary Venomics Lab: www.venomicslab.com

TA-06. Centre for Ecological Sciences

Indian Institute of Sciences.

Bangalore 560012. Karnataka, India

[Mark Miller]

Hi Vivek,

Thanks for the question.

Jmodeltest2 has been superceded by modeltestng, and the authors recommend using the latter. However, both interfaces are available on CIPRES.

The discussion group for these codes is here: https://groups.google.com/g/modeltest-ng

Hope that helps.

Mark

[Vivek Suranse]

Dear Mark,

Apologies for the delay in reverting. Thanks a ton for your response. I will follow the manual for model selection.

Best,

Vivek

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