PhyML as windows command line tool

[PetraGutenbrunner]

Hi,

I would like to run PhyML on the Windows command line with setting the parameters as described in “7.2 Command-line interface” in phyml_manual_2012.pdf. However, it seems that this option is only supported for MacOS and Linux. For Windows as far as I can see only an interactive user interface (phyml.bat, PhyML-3.1_win32.exe) is provided, which is not suitable for pipeline integration.

Would there be a possibility to also provide a basic command line PhyML for Windows? It would be of great value. Many thanks.

Best regards,
Petra Gutenbrunner

[stephaneguindon]

Dear Petra,
Have you tried installing PhyML through its Bioconda package? That might be the easiest way to get a recent version of PhyML run on Windows. Regards,

[PetraGutenbrunner]

Dear Stephane,

At the moment I've just downloaded the tool from http://www.atgc-montpellier.fr/phyml/binaries.php. I will try as you suggested, thank you! Best, Petra

[PetraGutenbrunner]

Moving back to this thread. I compiled PhyML based on the recent stable release for Windows, however, it seems there is still just the interactive command line version provided.

[stephaneguindon]

Can you tell me how you launch PhyML here?