This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Convert Nexus format to Newick format

Hi everyone!

I have just started with Perl and I need to convert my Nexus files into Newick format but I feel that it's too complicated for my level of knowledge to write this script, I think that I'm overthinking every time I try to write this script. Do someone know how I can convert all of my 1995 files into Newick format? Or a page where I can read how to convert files for beginners? I will be very grateful for your help.

perl nexus newick converter
• 11,411 views • link
updated by BlastedBadger BlastedBadger • written by ArusjakGevorgyan • ArusjakGevorgyan

Does it have to be a Perl module or you could try BioPython Phylo.convert instead?

• 0 views • link
written by Sej Modha Sej Modha

Thank you, I can try to read about it. But do you know if I have to write a python script with this converter function or it is build in BioPython?

• 0 views • link
written by ArusjakGevorgyan • ArusjakGevorgyan

2 answers

The bioconvert project can also perform this particular conversion (among many other).

• 0 views • link
written by BlastedBadger BlastedBadger

perhaps this little tools will do it TreeCon-Tools

• 0 views • link
written by lieven.sterck lieven.sterck

Are you sure about that? Only formats supported seem to be NH/NHX and TreeCon.

• 0 views • link
written by GenoMax GenoMax

ah, you might be right it only seems to support Newick format and not the Nexus.

I think using treeCon you might be able to switch formats as well but that is becoming quite cumbersome ;-)

• 0 views • link
written by lieven.sterck lieven.sterck

Log in to answer this question.

More posts like this