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Pas-Kapli / mptp

mPTP - a tool for single-locus species delimitation
GNU Affero General Public License v3.0
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Support more tree file and alignment file formats #70

Open lutteropp opened 8 years ago

lutteropp commented 8 years ago

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 commented 8 years ago

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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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 commented 8 years ago

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 commented 8 years ago

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. :)

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/Pas-Kapli/mptp/issues/70#issuecomment-208215225

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 commented 8 years ago

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.