Convert Nexus format to Newick format

Question

[ArusjakGevorgyan]

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.

[Sej Modha]

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

[ArusjakGevorgyan]

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?

[GenoMax]

http://phylogeny.lirmm.fr/phylo_cgi/data_converter.cgi
https://www.kmeverson.org/blog/convert-among-alignment-file-formats-nexus-phylip-fasta-etc

[ArusjakGevorgyan]

Thank you so much, I will read about this.

Answer 1

[BlastedBadger]

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

Answer 2

[lieven.sterck]

perhaps this little tools will do it TreeCon-Tools

[ArusjakGevorgyan]

Thank you so much for your help.

[GenoMax]

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

[lieven.sterck]

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 ;-)