Command line access to FigTree

[Pandurang Kolekar]

Hi Andrew,

Thanks for the FigTree!

How to generate the PDF or image file from Newick file from FigTree using command line? If there is any provision to access FigTree through command line or program, please let me know. I want to create pdfs and images for huge set of Newick files.The command line utility of FigTree would be of great help.

Thanking you,

Best regards,

Pandurang

[Andrew Rambaut]

If you download the Linux/UNIX version there is a command line script in the bin/ folder. If you do ‘figtree -help’ you will see the options.

Basically this acts as a pipe - you read a tree in and it will produce a graphic file out. If you want to do any formatting you will need to add

a ‘FigTree’ block to the end of the Nexus file. One way of doing this is loading one tree in to the GUI version, setting everything and then

saving. Paste this block to to the end of each tree you want to run through the command line version.

Andrew

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Andrew Rambaut 

Institute for Evolutionary Biology | Centre for Infection, Immunity & Evolution 

Ashworth Laboratories, University of Edinburgh, Edinburgh, EH3 9JT, UK

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[Pandurang Kolekar]

Thanks Andrew!

I will try it out in Linux. I am also curious to know whether there is such utility in Windows operating system.

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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   Best regards,

   Pandurang

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[Pandurang Kolekar]

I just tried out in Windows, it works fine!

Thanks a lot!

[Andrew Rambaut]

It is Java so it should work fine on Windows. But if you get the Linux version you have direct access to the

jar file. You can run it using a command line like:

java -jar figtree.jar -help

Andrew

On 6 Dec 2013, at 11:58, Pandurang Kolekar <panduran...@gmail.com> wrote:

I will try it out in Linux. I am also curious to know whether there is such utility in Windows operating system.

[Pandurang Kolekar]

Yes, right sir, did the same way.

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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