Pargenes-export / ASTRAL / ASTER

[anwesha mimi Saha]

Dear Dr. Morel,

Good morning,

I appreciate your help regarding PARGENES. I have a question regarding the Pargenes-export command and using ASTRAL/ASTER with the Pargenes output. I went through the installation and execution guide.  

How to prepare the gene (best-ml-tree) trees for ASTRAL? I can not find the command Pargenes-export when I type --help (See the attached pargenes--help.log)

I would be glad if you could help me with this. I am very new to using Python-based computational analysis.

Best regards,

Ms. Anwesha Saha

PhD Student

Institute of Paleobiology

Polish Academy of Sciences

Warsaw, Poland

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Centre for New Technologies (CeNT)

Laboratory for Palaeogenetics and Conservation Genetics.

University of Warsaw

Poland

Warsaw, Poland

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MRes Biodiversity, Evolution & Conservation, UK

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Former Research Fellow

Ashoka Trust for Research in Ecology & Environment (ATREE)

Bangalore, India

[Benoit Morel]

Hello,

The easiest way to run Astral is to run your gene tree inferences with pargenes, but add  "--use-astral" to the pargenes command (see Command line · BenoitMorel/ParGenes Wiki)

The export command is mostly to only extract important files and allow you to remove all the intermediate files that might be useless. It is a separate script, which is why you dont see it in pargenes.py --help (see Exporting relevant files · BenoitMorel/ParGenes Wiki). I dont remember the file structure after an export, but I don't think it perfectly fits Astral input directly.

I hope it helps, don't hesitate if I didn't answer your question

Benoit