Question: Convert Nexus format to Newick format
0
gravatar for ArusjakGevorgyan
2.5 years ago by
Sweden
ArusjakGevorgyan20 wrote:

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.

newick nexus converter perl • 3.2k views
ADD COMMENTlink modified 11 months ago by BlastedBadger90 • written 2.5 years ago by ArusjakGevorgyan20

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

ADD REPLYlink written 2.5 years ago by Sej Modha4.7k

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?

ADD REPLYlink written 2.5 years ago by ArusjakGevorgyan20

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

ADD REPLYlink written 2.5 years ago by genomax87k

Thank you so much, I will read about this.

ADD REPLYlink written 2.5 years ago by ArusjakGevorgyan20
0
gravatar for lieven.sterck
2.5 years ago by
lieven.sterck8.2k
VIB, Ghent, Belgium
lieven.sterck8.2k wrote:

perhaps this little tools will do it TreeCon-Tools

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by lieven.sterck8.2k

Thank you so much for your help.

ADD REPLYlink written 2.5 years ago by ArusjakGevorgyan20

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

ADD REPLYlink written 2.5 years ago by genomax87k

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 ;-)

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by lieven.sterck8.2k
0
gravatar for BlastedBadger
11 months ago by
Thule
BlastedBadger90 wrote:

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

ADD COMMENTlink written 11 months ago by BlastedBadger90
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