Support more tree file and alignment file formats

[lutteropp]

I know there exist other programs that can do the conversions. However, it can get very time-consuming to set up an analysis pipeline where each program requires another file format. :-(

Maybe we could have a script that converts all those widely used formats into the ones we want and call it directly from within mPTP?

It would make life much easier if all bioinformatics software would do this!

[stamatak]

this will be a lot of work, do you want to write this script yourself?

also calling a script from within a C code is not very elegant either
... in principle it should be able to handle more tree formats, since
80% of the ptp questions we are getting are due to incorrect tree
formats ... maybe just some more verbose error messages or guessing of
what the input format provided by the user is will do ...

alexis

On 10.04.2016 14:23, Sarah Lutteropp wrote:

I know there exist other program that can do the conversions. However,
it can get very time-consuming to set up an analysis pipeline where each
program requires another file format. :-(

Maybe we can have a script that converts all those widely used formats
into the ones we want and call it directly from within mPTP?

It would make life much easier if all bioinformatics software would do this.

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#70

Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[lutteropp]

I think the cleanest way would be to create an external C library that we can then use and make it publicly available with good documentation. :)

[stamatak]

yes :-)

alexis

On 11.04.2016 10:05, Sarah Lutteropp wrote:

I think the cleanest way would be to create an external C library that
we can then use and make it publicly available with good documentation. :)

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#70 (comment)

Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[xflouris]

Hi Alexi and Sarah,
sarah : we can extend newick-tools and extract a library out of it -- but it shouldn't be of priority now. For the mptp application (console-based) I think the newick format is sufficient.. fixing the error messages a bit will be sufficient for the average linux user.

For the web-service, we can add some more tree formats. I'm currently using David Dao's excellent JS newick parser and viewer.. and there's some more JS parsers/viewers for nexus.